diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle index 9e4097773..86bcd4858 100644 Binary files a/.doctrees/environment.pickle and b/.doctrees/environment.pickle differ diff --git a/.doctrees/nbsphinx/notebooks/nmodl-kinetic-schemes.ipynb b/.doctrees/nbsphinx/notebooks/nmodl-kinetic-schemes.ipynb index a3b84c640..9423ac0c3 100644 --- a/.doctrees/nbsphinx/notebooks/nmodl-kinetic-schemes.ipynb +++ b/.doctrees/nbsphinx/notebooks/nmodl-kinetic-schemes.ipynb @@ -152,10 +152,10 @@ "execution_count": 1, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:09.233551Z", - "iopub.status.busy": "2024-07-05T14:21:09.233360Z", - "iopub.status.idle": "2024-07-05T14:21:09.971964Z", - "shell.execute_reply": "2024-07-05T14:21:09.971253Z" + "iopub.execute_input": "2024-07-08T14:19:11.343181Z", + "iopub.status.busy": "2024-07-08T14:19:11.342948Z", + "iopub.status.idle": "2024-07-08T14:19:12.142002Z", + "shell.execute_reply": "2024-07-08T14:19:12.141214Z" } }, "outputs": [], @@ -169,10 +169,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:09.975041Z", - "iopub.status.busy": "2024-07-05T14:21:09.974634Z", - "iopub.status.idle": "2024-07-05T14:21:10.001923Z", - "shell.execute_reply": "2024-07-05T14:21:10.001287Z" + "iopub.execute_input": "2024-07-08T14:19:12.145153Z", + "iopub.status.busy": "2024-07-08T14:19:12.144926Z", + "iopub.status.idle": "2024-07-08T14:19:12.173471Z", + "shell.execute_reply": "2024-07-08T14:19:12.172816Z" } }, "outputs": [], @@ -277,10 +277,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:10.005002Z", - "iopub.status.busy": "2024-07-05T14:21:10.004689Z", - "iopub.status.idle": "2024-07-05T14:21:10.009712Z", - "shell.execute_reply": "2024-07-05T14:21:10.009056Z" + "iopub.execute_input": "2024-07-08T14:19:12.176565Z", + "iopub.status.busy": "2024-07-08T14:19:12.176282Z", + "iopub.status.idle": "2024-07-08T14:19:12.181063Z", + "shell.execute_reply": "2024-07-08T14:19:12.180392Z" } }, "outputs": [ @@ -323,10 +323,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:10.038573Z", - "iopub.status.busy": "2024-07-05T14:21:10.038045Z", - "iopub.status.idle": "2024-07-05T14:21:10.041944Z", - "shell.execute_reply": "2024-07-05T14:21:10.041310Z" + "iopub.execute_input": "2024-07-08T14:19:12.212484Z", + "iopub.status.busy": "2024-07-08T14:19:12.212210Z", + "iopub.status.idle": "2024-07-08T14:19:12.217225Z", + "shell.execute_reply": "2024-07-08T14:19:12.216517Z" } }, "outputs": [ @@ -367,10 +367,10 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:10.044424Z", - "iopub.status.busy": "2024-07-05T14:21:10.044080Z", - "iopub.status.idle": "2024-07-05T14:21:10.047715Z", - "shell.execute_reply": "2024-07-05T14:21:10.047069Z" + "iopub.execute_input": "2024-07-08T14:19:12.219699Z", + "iopub.status.busy": "2024-07-08T14:19:12.219477Z", + "iopub.status.idle": "2024-07-08T14:19:12.223731Z", + "shell.execute_reply": "2024-07-08T14:19:12.223002Z" }, "scrolled": true }, @@ -412,10 +412,10 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:10.050110Z", - "iopub.status.busy": "2024-07-05T14:21:10.049673Z", - "iopub.status.idle": "2024-07-05T14:21:10.053448Z", - "shell.execute_reply": "2024-07-05T14:21:10.052823Z" + "iopub.execute_input": "2024-07-08T14:19:12.226274Z", + "iopub.status.busy": "2024-07-08T14:19:12.226063Z", + "iopub.status.idle": "2024-07-08T14:19:12.230139Z", + "shell.execute_reply": "2024-07-08T14:19:12.229453Z" }, "scrolled": true }, @@ -459,10 +459,10 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:10.055917Z", - "iopub.status.busy": "2024-07-05T14:21:10.055579Z", - "iopub.status.idle": "2024-07-05T14:21:10.059677Z", - "shell.execute_reply": "2024-07-05T14:21:10.059013Z" + "iopub.execute_input": "2024-07-08T14:19:12.233438Z", + "iopub.status.busy": "2024-07-08T14:19:12.232862Z", + "iopub.status.idle": "2024-07-08T14:19:12.238022Z", + "shell.execute_reply": "2024-07-08T14:19:12.237325Z" } }, "outputs": [ diff --git a/.doctrees/nbsphinx/notebooks/nmodl-python-tutorial.ipynb b/.doctrees/nbsphinx/notebooks/nmodl-python-tutorial.ipynb index 41d803bba..6bbe2e92e 100644 --- a/.doctrees/nbsphinx/notebooks/nmodl-python-tutorial.ipynb +++ b/.doctrees/nbsphinx/notebooks/nmodl-python-tutorial.ipynb @@ -30,10 +30,10 @@ "execution_count": 1, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:14.945002Z", - "iopub.status.busy": "2024-07-05T14:21:14.944804Z", - "iopub.status.idle": "2024-07-05T14:21:15.691254Z", - "shell.execute_reply": "2024-07-05T14:21:15.690532Z" + "iopub.execute_input": "2024-07-08T14:19:17.773745Z", + "iopub.status.busy": "2024-07-08T14:19:17.773508Z", + "iopub.status.idle": "2024-07-08T14:19:18.583317Z", + "shell.execute_reply": "2024-07-08T14:19:18.582499Z" } }, "outputs": [], @@ -63,10 +63,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.694514Z", - "iopub.status.busy": "2024-07-05T14:21:15.694056Z", - "iopub.status.idle": "2024-07-05T14:21:15.718735Z", - "shell.execute_reply": "2024-07-05T14:21:15.718124Z" + "iopub.execute_input": "2024-07-08T14:19:18.586574Z", + "iopub.status.busy": "2024-07-08T14:19:18.586304Z", + "iopub.status.idle": "2024-07-08T14:19:18.613678Z", + "shell.execute_reply": "2024-07-08T14:19:18.612926Z" } }, "outputs": [], @@ -86,10 +86,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.721535Z", - "iopub.status.busy": "2024-07-05T14:21:15.721147Z", - "iopub.status.idle": "2024-07-05T14:21:15.724718Z", - "shell.execute_reply": "2024-07-05T14:21:15.724167Z" + "iopub.execute_input": "2024-07-08T14:19:18.616835Z", + "iopub.status.busy": "2024-07-08T14:19:18.616603Z", + "iopub.status.idle": "2024-07-08T14:19:18.620503Z", + "shell.execute_reply": "2024-07-08T14:19:18.619909Z" } }, "outputs": [], @@ -152,10 +152,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.727245Z", - "iopub.status.busy": "2024-07-05T14:21:15.726869Z", - "iopub.status.idle": "2024-07-05T14:21:15.731580Z", - "shell.execute_reply": "2024-07-05T14:21:15.730940Z" + "iopub.execute_input": "2024-07-08T14:19:18.623065Z", + "iopub.status.busy": "2024-07-08T14:19:18.622848Z", + "iopub.status.idle": "2024-07-08T14:19:18.627437Z", + "shell.execute_reply": "2024-07-08T14:19:18.626783Z" } }, "outputs": [], @@ -183,10 +183,10 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.733982Z", - "iopub.status.busy": "2024-07-05T14:21:15.733638Z", - "iopub.status.idle": "2024-07-05T14:21:15.737180Z", - "shell.execute_reply": "2024-07-05T14:21:15.736567Z" + "iopub.execute_input": "2024-07-08T14:19:18.630025Z", + "iopub.status.busy": "2024-07-08T14:19:18.629756Z", + "iopub.status.idle": "2024-07-08T14:19:18.633773Z", + "shell.execute_reply": "2024-07-08T14:19:18.633051Z" } }, "outputs": [ @@ -235,10 +235,10 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.739589Z", - "iopub.status.busy": "2024-07-05T14:21:15.739255Z", - "iopub.status.idle": "2024-07-05T14:21:15.743109Z", - "shell.execute_reply": "2024-07-05T14:21:15.742499Z" + "iopub.execute_input": "2024-07-08T14:19:18.636311Z", + "iopub.status.busy": "2024-07-08T14:19:18.636114Z", + "iopub.status.idle": "2024-07-08T14:19:18.640682Z", + "shell.execute_reply": "2024-07-08T14:19:18.640124Z" } }, "outputs": [], @@ -260,10 +260,10 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.745584Z", - "iopub.status.busy": "2024-07-05T14:21:15.745100Z", - "iopub.status.idle": "2024-07-05T14:21:15.748776Z", - "shell.execute_reply": "2024-07-05T14:21:15.748153Z" + "iopub.execute_input": "2024-07-08T14:19:18.643170Z", + "iopub.status.busy": "2024-07-08T14:19:18.642970Z", + "iopub.status.idle": "2024-07-08T14:19:18.646781Z", + "shell.execute_reply": "2024-07-08T14:19:18.646083Z" } }, "outputs": [ @@ -297,10 +297,10 @@ "execution_count": 8, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.751231Z", - "iopub.status.busy": "2024-07-05T14:21:15.750748Z", - "iopub.status.idle": "2024-07-05T14:21:15.758064Z", - "shell.execute_reply": "2024-07-05T14:21:15.757435Z" + "iopub.execute_input": "2024-07-08T14:19:18.649463Z", + "iopub.status.busy": "2024-07-08T14:19:18.649062Z", + "iopub.status.idle": "2024-07-08T14:19:18.656877Z", + "shell.execute_reply": "2024-07-08T14:19:18.656192Z" } }, "outputs": [ @@ -365,10 +365,10 @@ "execution_count": 9, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.760443Z", - "iopub.status.busy": "2024-07-05T14:21:15.760107Z", - "iopub.status.idle": "2024-07-05T14:21:15.764246Z", - "shell.execute_reply": "2024-07-05T14:21:15.763621Z" + "iopub.execute_input": "2024-07-08T14:19:18.659462Z", + "iopub.status.busy": "2024-07-08T14:19:18.659251Z", + "iopub.status.idle": "2024-07-08T14:19:18.663832Z", + "shell.execute_reply": "2024-07-08T14:19:18.663176Z" } }, "outputs": [ @@ -416,10 +416,10 @@ "execution_count": 10, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.766684Z", - "iopub.status.busy": "2024-07-05T14:21:15.766443Z", - "iopub.status.idle": "2024-07-05T14:21:15.769766Z", - "shell.execute_reply": "2024-07-05T14:21:15.769138Z" + "iopub.execute_input": "2024-07-08T14:19:18.666269Z", + "iopub.status.busy": "2024-07-08T14:19:18.666074Z", + "iopub.status.idle": "2024-07-08T14:19:18.669857Z", + "shell.execute_reply": "2024-07-08T14:19:18.669188Z" } }, "outputs": [], @@ -441,10 +441,10 @@ "execution_count": 11, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.772077Z", - "iopub.status.busy": "2024-07-05T14:21:15.771878Z", - "iopub.status.idle": "2024-07-05T14:21:15.775486Z", - "shell.execute_reply": "2024-07-05T14:21:15.774822Z" + "iopub.execute_input": "2024-07-08T14:19:18.672469Z", + "iopub.status.busy": "2024-07-08T14:19:18.672262Z", + "iopub.status.idle": "2024-07-08T14:19:18.676241Z", + "shell.execute_reply": "2024-07-08T14:19:18.675532Z" } }, "outputs": [ @@ -510,10 +510,10 @@ "execution_count": 12, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.778089Z", - "iopub.status.busy": "2024-07-05T14:21:15.777704Z", - "iopub.status.idle": "2024-07-05T14:21:15.780991Z", - "shell.execute_reply": "2024-07-05T14:21:15.780332Z" + "iopub.execute_input": "2024-07-08T14:19:18.678863Z", + "iopub.status.busy": "2024-07-08T14:19:18.678417Z", + "iopub.status.idle": "2024-07-08T14:19:18.682345Z", + "shell.execute_reply": "2024-07-08T14:19:18.681608Z" } }, "outputs": [ @@ -548,10 +548,10 @@ "execution_count": 13, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.783522Z", - "iopub.status.busy": "2024-07-05T14:21:15.783156Z", - "iopub.status.idle": "2024-07-05T14:21:15.786554Z", - "shell.execute_reply": "2024-07-05T14:21:15.785874Z" + "iopub.execute_input": "2024-07-08T14:19:18.684840Z", + "iopub.status.busy": "2024-07-08T14:19:18.684633Z", + "iopub.status.idle": "2024-07-08T14:19:18.688452Z", + "shell.execute_reply": "2024-07-08T14:19:18.687745Z" } }, "outputs": [ @@ -584,10 +584,10 @@ "execution_count": 14, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.789101Z", - "iopub.status.busy": "2024-07-05T14:21:15.788742Z", - "iopub.status.idle": "2024-07-05T14:21:15.792205Z", - "shell.execute_reply": "2024-07-05T14:21:15.791559Z" + "iopub.execute_input": "2024-07-08T14:19:18.690987Z", + "iopub.status.busy": "2024-07-08T14:19:18.690790Z", + "iopub.status.idle": "2024-07-08T14:19:18.694530Z", + "shell.execute_reply": "2024-07-08T14:19:18.693795Z" } }, "outputs": [ @@ -622,10 +622,10 @@ "execution_count": 15, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.794735Z", - "iopub.status.busy": "2024-07-05T14:21:15.794357Z", - "iopub.status.idle": "2024-07-05T14:21:15.798261Z", - "shell.execute_reply": "2024-07-05T14:21:15.797605Z" + "iopub.execute_input": "2024-07-08T14:19:18.696897Z", + "iopub.status.busy": "2024-07-08T14:19:18.696703Z", + "iopub.status.idle": "2024-07-08T14:19:18.701003Z", + "shell.execute_reply": "2024-07-08T14:19:18.700285Z" } }, "outputs": [ @@ -669,10 +669,10 @@ "execution_count": 16, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.800806Z", - "iopub.status.busy": "2024-07-05T14:21:15.800446Z", - "iopub.status.idle": "2024-07-05T14:21:15.805642Z", - "shell.execute_reply": "2024-07-05T14:21:15.804987Z" + "iopub.execute_input": "2024-07-08T14:19:18.703593Z", + "iopub.status.busy": "2024-07-08T14:19:18.703371Z", + "iopub.status.idle": "2024-07-08T14:19:18.709089Z", + "shell.execute_reply": "2024-07-08T14:19:18.708371Z" } }, "outputs": [ @@ -733,10 +733,10 @@ "execution_count": 17, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.808183Z", - "iopub.status.busy": "2024-07-05T14:21:15.807809Z", - "iopub.status.idle": "2024-07-05T14:21:15.811249Z", - "shell.execute_reply": "2024-07-05T14:21:15.810663Z" + "iopub.execute_input": "2024-07-08T14:19:18.711847Z", + "iopub.status.busy": "2024-07-08T14:19:18.711608Z", + "iopub.status.idle": "2024-07-08T14:19:18.715630Z", + "shell.execute_reply": "2024-07-08T14:19:18.714908Z" } }, "outputs": [], @@ -761,10 +761,10 @@ "execution_count": 18, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.813704Z", - "iopub.status.busy": "2024-07-05T14:21:15.813344Z", - "iopub.status.idle": "2024-07-05T14:21:15.823586Z", - "shell.execute_reply": "2024-07-05T14:21:15.823016Z" + "iopub.execute_input": "2024-07-08T14:19:18.718205Z", + "iopub.status.busy": "2024-07-08T14:19:18.717990Z", + "iopub.status.idle": "2024-07-08T14:19:18.728725Z", + "shell.execute_reply": "2024-07-08T14:19:18.728117Z" } }, "outputs": [], @@ -857,10 +857,10 @@ "execution_count": 19, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.826009Z", - "iopub.status.busy": "2024-07-05T14:21:15.825647Z", - "iopub.status.idle": "2024-07-05T14:21:15.829100Z", - "shell.execute_reply": "2024-07-05T14:21:15.828448Z" + "iopub.execute_input": "2024-07-08T14:19:18.731260Z", + "iopub.status.busy": "2024-07-08T14:19:18.731026Z", + "iopub.status.idle": "2024-07-08T14:19:18.735329Z", + "shell.execute_reply": "2024-07-08T14:19:18.734631Z" } }, "outputs": [ @@ -897,10 +897,10 @@ "execution_count": 20, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.831705Z", - "iopub.status.busy": "2024-07-05T14:21:15.831344Z", - "iopub.status.idle": "2024-07-05T14:21:15.836721Z", - "shell.execute_reply": "2024-07-05T14:21:15.836059Z" + "iopub.execute_input": "2024-07-08T14:19:18.737758Z", + "iopub.status.busy": "2024-07-08T14:19:18.737554Z", + "iopub.status.idle": "2024-07-08T14:19:18.743435Z", + "shell.execute_reply": "2024-07-08T14:19:18.742749Z" } }, "outputs": [ diff --git a/.doctrees/nbsphinx/notebooks/nmodl-sympy-conductance.ipynb b/.doctrees/nbsphinx/notebooks/nmodl-sympy-conductance.ipynb index c67b5c06f..6e10fa6ad 100644 --- a/.doctrees/nbsphinx/notebooks/nmodl-sympy-conductance.ipynb +++ b/.doctrees/nbsphinx/notebooks/nmodl-sympy-conductance.ipynb @@ -86,10 +86,10 @@ "execution_count": 1, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:17.997610Z", - "iopub.status.busy": "2024-07-05T14:21:17.997078Z", - "iopub.status.idle": "2024-07-05T14:21:18.738526Z", - "shell.execute_reply": "2024-07-05T14:21:18.737746Z" + "iopub.execute_input": "2024-07-08T14:19:21.317356Z", + "iopub.status.busy": "2024-07-08T14:19:21.316786Z", + "iopub.status.idle": "2024-07-08T14:19:22.121495Z", + "shell.execute_reply": "2024-07-08T14:19:22.120676Z" } }, "outputs": [], @@ -103,10 +103,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:18.741634Z", - "iopub.status.busy": "2024-07-05T14:21:18.741215Z", - "iopub.status.idle": "2024-07-05T14:21:18.768427Z", - "shell.execute_reply": "2024-07-05T14:21:18.767699Z" + "iopub.execute_input": "2024-07-08T14:19:22.125074Z", + "iopub.status.busy": "2024-07-08T14:19:22.124482Z", + "iopub.status.idle": "2024-07-08T14:19:22.153146Z", + "shell.execute_reply": "2024-07-08T14:19:22.152468Z" } }, "outputs": [], @@ -149,10 +149,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:18.771220Z", - "iopub.status.busy": "2024-07-05T14:21:18.770972Z", - "iopub.status.idle": "2024-07-05T14:21:19.027232Z", - "shell.execute_reply": "2024-07-05T14:21:19.026555Z" + "iopub.execute_input": "2024-07-08T14:19:22.156578Z", + "iopub.status.busy": "2024-07-08T14:19:22.156052Z", + "iopub.status.idle": "2024-07-08T14:19:22.440666Z", + "shell.execute_reply": "2024-07-08T14:19:22.439889Z" } }, "outputs": [ @@ -196,10 +196,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:19.029882Z", - "iopub.status.busy": "2024-07-05T14:21:19.029540Z", - "iopub.status.idle": "2024-07-05T14:21:19.176209Z", - "shell.execute_reply": "2024-07-05T14:21:19.175391Z" + "iopub.execute_input": "2024-07-08T14:19:22.443723Z", + "iopub.status.busy": "2024-07-08T14:19:22.443084Z", + "iopub.status.idle": "2024-07-08T14:19:22.597116Z", + "shell.execute_reply": "2024-07-08T14:19:22.596399Z" } }, "outputs": [ @@ -243,10 +243,10 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:19.179397Z", - "iopub.status.busy": "2024-07-05T14:21:19.178856Z", - "iopub.status.idle": "2024-07-05T14:21:19.187019Z", - "shell.execute_reply": "2024-07-05T14:21:19.186366Z" + "iopub.execute_input": "2024-07-08T14:19:22.599924Z", + "iopub.status.busy": "2024-07-08T14:19:22.599697Z", + "iopub.status.idle": "2024-07-08T14:19:22.608506Z", + "shell.execute_reply": "2024-07-08T14:19:22.607749Z" } }, "outputs": [ @@ -290,10 +290,10 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:19.189557Z", - "iopub.status.busy": "2024-07-05T14:21:19.189065Z", - "iopub.status.idle": "2024-07-05T14:21:19.206236Z", - "shell.execute_reply": "2024-07-05T14:21:19.205688Z" + "iopub.execute_input": "2024-07-08T14:19:22.611253Z", + "iopub.status.busy": "2024-07-08T14:19:22.611025Z", + "iopub.status.idle": "2024-07-08T14:19:22.629729Z", + "shell.execute_reply": "2024-07-08T14:19:22.629073Z" } }, "outputs": [ @@ -337,10 +337,10 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:19.208598Z", - "iopub.status.busy": "2024-07-05T14:21:19.208304Z", - "iopub.status.idle": "2024-07-05T14:21:19.331870Z", - "shell.execute_reply": "2024-07-05T14:21:19.331230Z" + "iopub.execute_input": "2024-07-08T14:19:22.632430Z", + "iopub.status.busy": "2024-07-08T14:19:22.632200Z", + "iopub.status.idle": "2024-07-08T14:19:22.762561Z", + "shell.execute_reply": "2024-07-08T14:19:22.761830Z" } }, "outputs": [ @@ -400,10 +400,10 @@ "execution_count": 8, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:19.334574Z", - "iopub.status.busy": "2024-07-05T14:21:19.334335Z", - "iopub.status.idle": "2024-07-05T14:21:19.433413Z", - "shell.execute_reply": "2024-07-05T14:21:19.432838Z" + "iopub.execute_input": "2024-07-08T14:19:22.765393Z", + "iopub.status.busy": "2024-07-08T14:19:22.765161Z", + "iopub.status.idle": "2024-07-08T14:19:22.870422Z", + "shell.execute_reply": "2024-07-08T14:19:22.869740Z" } }, "outputs": [ @@ -456,10 +456,10 @@ "execution_count": 9, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:19.435928Z", - "iopub.status.busy": "2024-07-05T14:21:19.435542Z", - "iopub.status.idle": "2024-07-05T14:21:19.506862Z", - "shell.execute_reply": "2024-07-05T14:21:19.506212Z" + "iopub.execute_input": "2024-07-08T14:19:22.873175Z", + "iopub.status.busy": "2024-07-08T14:19:22.872935Z", + "iopub.status.idle": "2024-07-08T14:19:22.948171Z", + "shell.execute_reply": "2024-07-08T14:19:22.947424Z" } }, "outputs": [ diff --git a/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-cnexp.ipynb b/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-cnexp.ipynb index 746260b4d..012809611 100644 --- a/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-cnexp.ipynb +++ b/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-cnexp.ipynb @@ -62,10 +62,10 @@ "execution_count": 1, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:21.082557Z", - "iopub.status.busy": "2024-07-05T14:21:21.081964Z", - "iopub.status.idle": "2024-07-05T14:21:21.826924Z", - "shell.execute_reply": "2024-07-05T14:21:21.826149Z" + "iopub.execute_input": "2024-07-08T14:19:24.812751Z", + "iopub.status.busy": "2024-07-08T14:19:24.812436Z", + "iopub.status.idle": "2024-07-08T14:19:25.623956Z", + "shell.execute_reply": "2024-07-08T14:19:25.623195Z" } }, "outputs": [], @@ -79,10 +79,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:21.830127Z", - "iopub.status.busy": "2024-07-05T14:21:21.829668Z", - "iopub.status.idle": "2024-07-05T14:21:21.857147Z", - "shell.execute_reply": "2024-07-05T14:21:21.856426Z" + "iopub.execute_input": "2024-07-08T14:19:25.627345Z", + "iopub.status.busy": "2024-07-08T14:19:25.627111Z", + "iopub.status.idle": "2024-07-08T14:19:25.658122Z", + "shell.execute_reply": "2024-07-08T14:19:25.657332Z" } }, "outputs": [], @@ -123,10 +123,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:21.859819Z", - "iopub.status.busy": "2024-07-05T14:21:21.859566Z", - "iopub.status.idle": "2024-07-05T14:21:22.307680Z", - "shell.execute_reply": "2024-07-05T14:21:22.306951Z" + "iopub.execute_input": "2024-07-08T14:19:25.661405Z", + "iopub.status.busy": "2024-07-08T14:19:25.661126Z", + "iopub.status.idle": "2024-07-08T14:19:26.125710Z", + "shell.execute_reply": "2024-07-08T14:19:26.124931Z" } }, "outputs": [ @@ -165,10 +165,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:22.310411Z", - "iopub.status.busy": "2024-07-05T14:21:22.309967Z", - "iopub.status.idle": "2024-07-05T14:21:22.445669Z", - "shell.execute_reply": "2024-07-05T14:21:22.444989Z" + "iopub.execute_input": "2024-07-08T14:19:26.128804Z", + "iopub.status.busy": "2024-07-08T14:19:26.128316Z", + "iopub.status.idle": "2024-07-08T14:19:26.268524Z", + "shell.execute_reply": "2024-07-08T14:19:26.267745Z" } }, "outputs": [ @@ -207,10 +207,10 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:22.448469Z", - "iopub.status.busy": "2024-07-05T14:21:22.448076Z", - "iopub.status.idle": "2024-07-05T14:21:22.679259Z", - "shell.execute_reply": "2024-07-05T14:21:22.678593Z" + "iopub.execute_input": "2024-07-08T14:19:26.271283Z", + "iopub.status.busy": "2024-07-08T14:19:26.271054Z", + "iopub.status.idle": "2024-07-08T14:19:26.510893Z", + "shell.execute_reply": "2024-07-08T14:19:26.510102Z" } }, "outputs": [ @@ -255,10 +255,10 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:22.682003Z", - "iopub.status.busy": "2024-07-05T14:21:22.681602Z", - "iopub.status.idle": "2024-07-05T14:21:22.873830Z", - "shell.execute_reply": "2024-07-05T14:21:22.873103Z" + "iopub.execute_input": "2024-07-08T14:19:26.513860Z", + "iopub.status.busy": "2024-07-08T14:19:26.513445Z", + "iopub.status.idle": "2024-07-08T14:19:26.712459Z", + "shell.execute_reply": "2024-07-08T14:19:26.711798Z" } }, "outputs": [ @@ -297,10 +297,10 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:22.876732Z", - "iopub.status.busy": "2024-07-05T14:21:22.876316Z", - "iopub.status.idle": "2024-07-05T14:21:24.273155Z", - "shell.execute_reply": "2024-07-05T14:21:24.272465Z" + "iopub.execute_input": "2024-07-08T14:19:26.715318Z", + "iopub.status.busy": "2024-07-08T14:19:26.714907Z", + "iopub.status.idle": "2024-07-08T14:19:28.190861Z", + "shell.execute_reply": "2024-07-08T14:19:28.190133Z" } }, "outputs": [ @@ -345,10 +345,10 @@ "execution_count": 8, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:24.276066Z", - "iopub.status.busy": "2024-07-05T14:21:24.275553Z", - "iopub.status.idle": "2024-07-05T14:21:26.074496Z", - "shell.execute_reply": "2024-07-05T14:21:26.073756Z" + "iopub.execute_input": "2024-07-08T14:19:28.193841Z", + "iopub.status.busy": "2024-07-08T14:19:28.193380Z", + "iopub.status.idle": "2024-07-08T14:19:30.056617Z", + "shell.execute_reply": "2024-07-08T14:19:30.055913Z" } }, "outputs": [ diff --git a/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-derivimplicit.ipynb b/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-derivimplicit.ipynb index 4c70d4e51..4a707599d 100644 --- a/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-derivimplicit.ipynb +++ b/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-derivimplicit.ipynb @@ -39,10 +39,10 @@ "execution_count": 1, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:27.681994Z", - "iopub.status.busy": "2024-07-05T14:21:27.681793Z", - "iopub.status.idle": "2024-07-05T14:21:28.433607Z", - "shell.execute_reply": "2024-07-05T14:21:28.432876Z" + "iopub.execute_input": "2024-07-08T14:19:32.049185Z", + "iopub.status.busy": "2024-07-08T14:19:32.048967Z", + "iopub.status.idle": "2024-07-08T14:19:32.852052Z", + "shell.execute_reply": "2024-07-08T14:19:32.851318Z" } }, "outputs": [], @@ -56,10 +56,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:28.436672Z", - "iopub.status.busy": "2024-07-05T14:21:28.436418Z", - "iopub.status.idle": "2024-07-05T14:21:28.463108Z", - "shell.execute_reply": "2024-07-05T14:21:28.462516Z" + "iopub.execute_input": "2024-07-08T14:19:32.855192Z", + "iopub.status.busy": "2024-07-08T14:19:32.854969Z", + "iopub.status.idle": "2024-07-08T14:19:32.884763Z", + "shell.execute_reply": "2024-07-08T14:19:32.883964Z" } }, "outputs": [], @@ -100,10 +100,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:28.465795Z", - "iopub.status.busy": "2024-07-05T14:21:28.465409Z", - "iopub.status.idle": "2024-07-05T14:21:28.939324Z", - "shell.execute_reply": "2024-07-05T14:21:28.938604Z" + "iopub.execute_input": "2024-07-08T14:19:32.888300Z", + "iopub.status.busy": "2024-07-08T14:19:32.887833Z", + "iopub.status.idle": "2024-07-08T14:19:33.384183Z", + "shell.execute_reply": "2024-07-08T14:19:33.383395Z" } }, "outputs": [ @@ -165,10 +165,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:28.941963Z", - "iopub.status.busy": "2024-07-05T14:21:28.941698Z", - "iopub.status.idle": "2024-07-05T14:21:29.157304Z", - "shell.execute_reply": "2024-07-05T14:21:29.156681Z" + "iopub.execute_input": "2024-07-08T14:19:33.387641Z", + "iopub.status.busy": "2024-07-08T14:19:33.387030Z", + "iopub.status.idle": "2024-07-08T14:19:33.615481Z", + "shell.execute_reply": "2024-07-08T14:19:33.614713Z" } }, "outputs": [ diff --git a/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-sparse.ipynb b/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-sparse.ipynb index de9653d18..558fe9452 100644 --- a/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-sparse.ipynb +++ b/.doctrees/nbsphinx/notebooks/nmodl-sympy-solver-sparse.ipynb @@ -39,10 +39,10 @@ "execution_count": 1, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:30.423828Z", - "iopub.status.busy": "2024-07-05T14:21:30.423267Z", - "iopub.status.idle": "2024-07-05T14:21:31.165732Z", - "shell.execute_reply": "2024-07-05T14:21:31.164876Z" + "iopub.execute_input": "2024-07-08T14:19:35.091365Z", + "iopub.status.busy": "2024-07-08T14:19:35.091139Z", + "iopub.status.idle": "2024-07-08T14:19:35.902205Z", + "shell.execute_reply": "2024-07-08T14:19:35.901295Z" } }, "outputs": [], @@ -56,10 +56,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:31.169076Z", - "iopub.status.busy": "2024-07-05T14:21:31.168671Z", - "iopub.status.idle": "2024-07-05T14:21:31.195296Z", - "shell.execute_reply": "2024-07-05T14:21:31.194695Z" + "iopub.execute_input": "2024-07-08T14:19:35.906761Z", + "iopub.status.busy": "2024-07-08T14:19:35.905989Z", + "iopub.status.idle": "2024-07-08T14:19:35.935381Z", + "shell.execute_reply": "2024-07-08T14:19:35.934578Z" } }, "outputs": [], @@ -100,10 +100,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:31.197866Z", - "iopub.status.busy": "2024-07-05T14:21:31.197551Z", - "iopub.status.idle": "2024-07-05T14:21:31.655770Z", - "shell.execute_reply": "2024-07-05T14:21:31.655040Z" + "iopub.execute_input": "2024-07-08T14:19:35.938636Z", + "iopub.status.busy": "2024-07-08T14:19:35.938316Z", + "iopub.status.idle": "2024-07-08T14:19:36.446881Z", + "shell.execute_reply": "2024-07-08T14:19:36.446144Z" } }, "outputs": [ @@ -165,10 +165,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:31.658505Z", - "iopub.status.busy": "2024-07-05T14:21:31.658062Z", - "iopub.status.idle": "2024-07-05T14:21:31.876405Z", - "shell.execute_reply": "2024-07-05T14:21:31.875701Z" + "iopub.execute_input": "2024-07-08T14:19:36.449568Z", + "iopub.status.busy": "2024-07-08T14:19:36.449291Z", + "iopub.status.idle": "2024-07-08T14:19:36.672354Z", + "shell.execute_reply": "2024-07-08T14:19:36.671576Z" } }, "outputs": [ diff --git a/doxygen/classnmodl_1_1codegen_1_1_codegen_neuron_cpp_visitor.html b/doxygen/classnmodl_1_1codegen_1_1_codegen_neuron_cpp_visitor.html index bc575c0ab..49977151b 100644 --- a/doxygen/classnmodl_1_1codegen_1_1_codegen_neuron_cpp_visitor.html +++ b/doxygen/classnmodl_1_1codegen_1_1_codegen_neuron_cpp_visitor.html @@ -1826,7 +1826,7 @@

-

Definition at line 1721 of file codegen_neuron_cpp_visitor.cpp.

+

Definition at line 1725 of file codegen_neuron_cpp_visitor.cpp.

@@ -1853,7 +1853,7 @@

-

Definition at line 1726 of file codegen_neuron_cpp_visitor.cpp.

+

Definition at line 1730 of file codegen_neuron_cpp_visitor.cpp.

@@ -2119,7 +2119,7 @@

nmodl::codegen::CodegenCppVisitor.

-

Definition at line 2058 of file codegen_neuron_cpp_visitor.cpp.

+

Definition at line 2064 of file codegen_neuron_cpp_visitor.cpp.

@@ -2151,7 +2151,7 @@

nmodl::codegen::CodegenCppVisitor.

-

Definition at line 2041 of file codegen_neuron_cpp_visitor.cpp.

+

Definition at line 2047 of file codegen_neuron_cpp_visitor.cpp.

@@ -2189,7 +2189,7 @@

nmodl::codegen::CodegenCppVisitor.

-

Definition at line 2009 of file codegen_neuron_cpp_visitor.cpp.

+

Definition at line 2015 of file codegen_neuron_cpp_visitor.cpp.

@@ -2221,7 +2221,7 @@

nmodl::codegen::CodegenCppVisitor.

-

Definition at line 1875 of file codegen_neuron_cpp_visitor.cpp.

+

Definition at line 1879 of file codegen_neuron_cpp_visitor.cpp.

@@ -2417,7 +2417,7 @@

nmodl::codegen::CodegenCppVisitor.

-

Definition at line 2031 of file codegen_neuron_cpp_visitor.cpp.

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Definition at line 2037 of file codegen_neuron_cpp_visitor.cpp.

@@ -2465,7 +2465,7 @@

nmodl::codegen::CodegenCppVisitor.

-

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nmodl::codegen::CodegenCppVisitor.

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nmodl::codegen::CodegenCppVisitor.

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nmodl::codegen::CodegenCppVisitor.

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nmodl::codegen::CodegenCppVisitor.

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nmodl::codegen::CodegenCppVisitor.

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nmodl::codegen::CodegenCppVisitor.

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nmodl::codegen::CodegenCppVisitor.

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nmodl::codegen::CodegenCppVisitor.

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nmodl::codegen::CodegenCppVisitor.

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nmodl::codegen::CodegenCppVisitor.

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nmodl::codegen::CodegenCppVisitor.

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nmodl::codegen::CodegenCppVisitor.

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@@ -4189,7 +4189,7 @@

nmodl::visitor::ConstVisitor.

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diff --git a/doxygen/codegen__neuron__cpp__visitor_8hpp_source.html b/doxygen/codegen__neuron__cpp__visitor_8hpp_source.html index bb878a15c..2b2e453b0 100644 --- a/doxygen/codegen__neuron__cpp__visitor_8hpp_source.html +++ b/doxygen/codegen__neuron__cpp__visitor_8hpp_source.html @@ -832,24 +832,24 @@
736 } // namespace nmodl
-
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_destructor
void print_nrn_destructor() override
Print nrn_destructor function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1560
-
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_cur_non_conductance_kernel
void print_nrn_cur_non_conductance_kernel() override
Print the nrn_cur kernel without NMODL conductance keyword provisions.
Definition: codegen_neuron_cpp_visitor.cpp:1807
+
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_destructor
void print_nrn_destructor() override
Print nrn_destructor function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1555
+
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_cur_non_conductance_kernel
void print_nrn_cur_non_conductance_kernel() override
Print the nrn_cur kernel without NMODL conductance keyword provisions.
Definition: codegen_neuron_cpp_visitor.cpp:1811
nmodl::codegen::CodegenNeuronCppVisitor::py_function_signature
std::string py_function_signature(const std::string &function_or_procedure_name) const
Get the signature of the npy <func_or_proc_name> function.
Definition: codegen_neuron_cpp_visitor.cpp:547
nmodl::codegen::IndexVariableInfo
Helper to represent information about index/int variables.
Definition: codegen_cpp_visitor.hpp:127
-
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_cur
void print_nrn_cur() override
Print nrn_cur / current update function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1881
-
nmodl::codegen::CodegenNeuronCppVisitor::print_macro_definitions
void print_macro_definitions()
Print all NEURON macros.
Definition: codegen_neuron_cpp_visitor.cpp:1937
+
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_cur
void print_nrn_cur() override
Print nrn_cur / current update function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1885
+
nmodl::codegen::CodegenNeuronCppVisitor::print_macro_definitions
void print_macro_definitions()
Print all NEURON macros.
Definition: codegen_neuron_cpp_visitor.cpp:1941
nmodl::codegen::CodegenCppVisitor::CodegenCppVisitor
CodegenCppVisitor(std::string mod_filename, const std::string &output_dir, std::string float_type, const bool optimize_ionvar_copies, std::unique_ptr< nmodl::utils::Blame > blame)
Constructs the C++ code generator visitor.
Definition: codegen_cpp_visitor.hpp:214
-
nmodl::codegen::CodegenNeuronCppVisitor::print_net_event_call
void print_net_event_call(const ast::FunctionCall &node) override
Print call to net_event.
Definition: codegen_neuron_cpp_visitor.cpp:2118
+
nmodl::codegen::CodegenNeuronCppVisitor::print_net_event_call
void print_net_event_call(const ast::FunctionCall &node) override
Print call to net_event.
Definition: codegen_neuron_cpp_visitor.cpp:2124
nmodl::codegen::CodegenNeuronCppVisitor::print_neuron_includes
void print_neuron_includes()
Print includes from NEURON.
Definition: codegen_neuron_cpp_visitor.cpp:767
-
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_init
void print_nrn_init(bool skip_init_check=true)
Print the nrn_init function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1500
+
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_init
void print_nrn_init(bool skip_init_check=true)
Print the nrn_init function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1495
nmodl::codegen::CodegenNeuronCppVisitor::print_hoc_py_wrapper_function_body
void print_hoc_py_wrapper_function_body(const ast::Block *function_or_procedure_block, InterpreterWrapper wrapper_type)
Definition: codegen_neuron_cpp_visitor.cpp:336
nmodl::codegen::CodegenNeuronCppVisitor::internal_method_arguments
std::string internal_method_arguments() override
Arguments for functions that are defined and used internally.
Definition: codegen_neuron_cpp_visitor.cpp:468
-
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_alloc
void print_nrn_alloc() override
Print nrn_alloc function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1566
+
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_alloc
void print_nrn_alloc() override
Print nrn_alloc function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1561
nmodl::codegen::CodegenNeuronCppVisitor::register_mechanism_arguments
std::string register_mechanism_arguments() const override
Arguments for register_mech or point_register_mech function.
Definition: codegen_neuron_cpp_visitor.cpp:521
nmodl::codegen::CodegenNeuronCppVisitor::position_of_int_var
int position_of_int_var(const std::string &name) const override
Determine the position in the data array for a given int variable.
Definition: codegen_neuron_cpp_visitor.cpp:76
- +
nmodl::codegen::CodegenNeuronCppVisitor::table_thread_function_name
std::string table_thread_function_name() const
Name of the threaded table checking function.
Definition: codegen_neuron_cpp_visitor.cpp:54
nmodl::codegen::CodegenNeuronCppVisitor::optimize_ion_variable_copies
bool optimize_ion_variable_copies() const override
Check if ion variable copies should be avoided.
Definition: codegen_neuron_cpp_visitor.cpp:100
nmodl::codegen::CodegenNeuronCppVisitor::hoc_function_name
std::string hoc_function_name(const std::string &function_or_procedure_name) const
All functions and procedures need a hoc <func_or_proc_name> to be available to the HOC interpreter.
Definition: codegen_neuron_cpp_visitor.cpp:526
@@ -859,22 +859,22 @@
symbol_table.hpp
Implement classes for representing symbol table at block and file scope.
nmodl::codegen::CodegenNeuronCppVisitor::backend_name
std::string backend_name() const override
Name of the code generation backend.
Definition: codegen_neuron_cpp_visitor.cpp:49
nmodl::codegen::CodegenNeuronCppVisitor::process_verbatim_text
std::string process_verbatim_text(std::string const &text) override
Process a verbatim block for possible variable renaming.
Definition: codegen_neuron_cpp_visitor.cpp:515
- -
nmodl::codegen::CodegenNeuronCppVisitor::print_g_unused
void print_g_unused() const override
Set g_unused (conductance) for NRN_PRCELLSTATE feature.
Definition: codegen_neuron_cpp_visitor.cpp:2031
-
nmodl::codegen::CodegenNeuronCppVisitor::visit_watch_statement
void visit_watch_statement(const ast::WatchStatement &node) override
TODO: Edit for NEURON.
Definition: codegen_neuron_cpp_visitor.cpp:2199
-
nmodl::codegen::CodegenNeuronCppVisitor::print_net_send_call
void print_net_send_call(const ast::FunctionCall &node) override
Print call to net_send.
Definition: codegen_neuron_cpp_visitor.cpp:2084
-
nmodl::codegen::CodegenNeuronCppVisitor::print_namespace_end
void print_namespace_end() override
Print end of namespaces.
Definition: codegen_neuron_cpp_visitor.cpp:2004
-
nmodl::codegen::CodegenNeuronCppVisitor::print_net_move_call
void print_net_move_call(const ast::FunctionCall &node) override
Print call to net_move.
Definition: codegen_neuron_cpp_visitor.cpp:2108
+ +
nmodl::codegen::CodegenNeuronCppVisitor::print_g_unused
void print_g_unused() const override
Set g_unused (conductance) for NRN_PRCELLSTATE feature.
Definition: codegen_neuron_cpp_visitor.cpp:2037
+
nmodl::codegen::CodegenNeuronCppVisitor::visit_watch_statement
void visit_watch_statement(const ast::WatchStatement &node) override
TODO: Edit for NEURON.
Definition: codegen_neuron_cpp_visitor.cpp:2205
+
nmodl::codegen::CodegenNeuronCppVisitor::print_net_send_call
void print_net_send_call(const ast::FunctionCall &node) override
Print call to net_send.
Definition: codegen_neuron_cpp_visitor.cpp:2090
+
nmodl::codegen::CodegenNeuronCppVisitor::print_namespace_end
void print_namespace_end() override
Print end of namespaces.
Definition: codegen_neuron_cpp_visitor.cpp:2010
+
nmodl::codegen::CodegenNeuronCppVisitor::print_net_move_call
void print_net_move_call(const ast::FunctionCall &node) override
Print call to net_move.
Definition: codegen_neuron_cpp_visitor.cpp:2114
nmodl::codegen::CodegenNeuronCppVisitor::thread_variable_name
std::string thread_variable_name(const ThreadVariableInfo &var_info, bool use_instance=true) const
Determine the C++ string to print for thread variables.
Definition: codegen_neuron_cpp_visitor.cpp:629
nmodl::SymbolType
parser::NmodlParser::symbol_type SymbolType
Definition: nmodl_utils.hpp:26
-
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_state
void print_nrn_state() override
Print nrn_state / state update function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1671
-
nmodl::codegen::CodegenNeuronCppVisitor::print_initial_block
void print_initial_block(const ast::InitialBlock *node)
Print the initial block.
Definition: codegen_neuron_cpp_visitor.cpp:1455
-
nmodl::codegen::CodegenNeuronCppVisitor::print_global_function_common_code
void print_global_function_common_code(BlockType type, const std::string &function_name="") override
Print common code for global functions like nrn_init, nrn_cur and nrn_state.
Definition: codegen_neuron_cpp_visitor.cpp:1477
+
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_state
void print_nrn_state() override
Print nrn_state / state update function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1675
+
nmodl::codegen::CodegenNeuronCppVisitor::print_initial_block
void print_initial_block(const ast::InitialBlock *node)
Print the initial block.
Definition: codegen_neuron_cpp_visitor.cpp:1450
+
nmodl::codegen::CodegenNeuronCppVisitor::print_global_function_common_code
void print_global_function_common_code(BlockType type, const std::string &function_name="") override
Print common code for global functions like nrn_init, nrn_cur and nrn_state.
Definition: codegen_neuron_cpp_visitor.cpp:1472
nmodl::codegen::CodegenNeuronCppVisitor::float_variable_name
std::string float_variable_name(const SymbolType &symbol, bool use_instance) const override
Determine the name of a float variable given its symbol.
Definition: codegen_neuron_cpp_visitor.cpp:581
nmodl::codegen::CodegenNeuronCppVisitor::print_function
void print_function(const ast::FunctionBlock &node) override
Print NMODL function in target backend code.
Definition: codegen_neuron_cpp_visitor.cpp:317
-
nmodl::codegen::CodegenNeuronCppVisitor::print_v_unused
void print_v_unused() const override
Set v_unused (voltage) for NRN_PRCELLSTATE feature.
Definition: codegen_neuron_cpp_visitor.cpp:2019
- +
nmodl::codegen::CodegenNeuronCppVisitor::print_v_unused
void print_v_unused() const override
Set v_unused (voltage) for NRN_PRCELLSTATE feature.
Definition: codegen_neuron_cpp_visitor.cpp:2025
+
nmodl::codegen::CodegenNeuronCppVisitor::functor_params
ParamVector functor_params() override
The parameters of the Newton solver "functor".
Definition: codegen_neuron_cpp_visitor.cpp:819
codegen_cpp_visitor.hpp
Visitor for printing C++ code compatible with legacy api of CoreNEURON
codegen_naming.hpp
@@ -882,72 +882,72 @@
nmodl::ast::InitialBlock
Represents a INITIAL block in the NMODL.
Definition: initial_block.hpp:49
nmodl::codegen::CodegenNeuronCppVisitor::print_point_process_function_definitions
void print_point_process_function_definitions()
Print POINT_PROCESS related functions Wrap external NEURON functions related to POINT_PROCESS mechani...
Definition: codegen_neuron_cpp_visitor.cpp:113
nmodl::ast::WatchStatement
Represent WATCH statement in NMODL.
Definition: watch_statement.hpp:39
-
nmodl::codegen::CodegenNeuronCppVisitor::print_neuron_global_variable_declarations
void print_neuron_global_variable_declarations()
Print extern declarations for neuron global variables.
Definition: codegen_neuron_cpp_visitor.cpp:1292
+
nmodl::codegen::CodegenNeuronCppVisitor::print_neuron_global_variable_declarations
void print_neuron_global_variable_declarations()
Print extern declarations for neuron global variables.
Definition: codegen_neuron_cpp_visitor.cpp:1287
nmodl::ast::BreakpointBlock
Represents a BREAKPOINT block in NMODL.
Definition: breakpoint_block.hpp:53
-
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_cur_conductance_kernel
void print_nrn_cur_conductance_kernel(const ast::BreakpointBlock &node) override
Print the nrn_cur kernel with NMODL conductance keyword provisions.
Definition: codegen_neuron_cpp_visitor.cpp:1768
+
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_cur_conductance_kernel
void print_nrn_cur_conductance_kernel(const ast::BreakpointBlock &node) override
Print the nrn_cur kernel with NMODL conductance keyword provisions.
Definition: codegen_neuron_cpp_visitor.cpp:1772
nmodl::codegen::CodegenNeuronCppVisitor::int_variable_name
std::string int_variable_name(const IndexVariableInfo &symbol, const std::string &name, bool use_instance) const override
Determine the name of an int variable given its symbol.
Definition: codegen_neuron_cpp_visitor.cpp:601
nmodl::codegen::InterpreterWrapper
InterpreterWrapper
Enum to switch between HOC and Python wrappers for functions and procedures defined in mechanisms.
Definition: codegen_neuron_cpp_visitor.hpp:50
-
nmodl::codegen::CodegenNeuronCppVisitor::print_namespace_begin
void print_namespace_begin() override
Print start of namespaces.
Definition: codegen_neuron_cpp_visitor.cpp:1999
+
nmodl::codegen::CodegenNeuronCppVisitor::print_namespace_begin
void print_namespace_begin() override
Print start of namespaces.
Definition: codegen_neuron_cpp_visitor.cpp:2005
nmodl::codegen::CodegenNeuronCppVisitor::print_global_variables_for_hoc
void print_global_variables_for_hoc() override
Print byte arrays that register scalar and vector variables for hoc interface.
Definition: codegen_neuron_cpp_visitor.cpp:981
nmodl::codegen::CodegenNeuronCppVisitor::print_standard_includes
void print_standard_includes() override
Print standard C/C++ includes.
Definition: codegen_neuron_cpp_visitor.cpp:751
nmodl::codegen::CodegenNeuronCppVisitor::codegen_thread_variables
std::vector< ThreadVariableInfo > codegen_thread_variables
GLOBAL variables in THREADSAFE MOD files that are not read-only are converted to thread variables.
Definition: codegen_neuron_cpp_visitor.hpp:98
-
nmodl::codegen::CodegenNeuronCppVisitor::print_mechanism_range_var_structure
void print_mechanism_range_var_structure(bool print_initializers) override
Print the structure that wraps all range and int variables required for the NMODL.
Definition: codegen_neuron_cpp_visitor.cpp:1299
+
nmodl::codegen::CodegenNeuronCppVisitor::print_mechanism_range_var_structure
void print_mechanism_range_var_structure(bool print_initializers) override
Print the structure that wraps all range and int variables required for the NMODL.
Definition: codegen_neuron_cpp_visitor.cpp:1294
nmodl::codegen::CodegenNeuronCppVisitor::print_procedure
void print_procedure(const ast::ProcedureBlock &node) override
Print NMODL procedure in target backend code.
Definition: codegen_neuron_cpp_visitor.cpp:312
nmodl::codegen::CodegenNeuronCppVisitor::add_variable_tqitem
void add_variable_tqitem(std::vector< IndexVariableInfo > &variables) override
Add the variable tqitem during get_int_variables.
Definition: codegen_neuron_cpp_visitor.cpp:454
code_printer.hpp
Helper class for printing C/C++ code.
nmodl::codegen::CodegenNeuronCppVisitor::hoc_function_signature
std::string hoc_function_signature(const std::string &function_or_procedure_name) const
Get the signature of the hoc <func_or_proc_name> function.
Definition: codegen_neuron_cpp_visitor.cpp:532
nmodl::codegen::CodegenNeuronCppVisitor::print_namespace_start
void print_namespace_start() override
Prints the start of the neuron namespace.
Definition: codegen_neuron_cpp_visitor.cpp:558
-
nmodl::codegen::CodegenNeuronCppVisitor::print_thread_variables_structure
void print_thread_variables_structure(bool print_initializers)
Print the data structure used to access thread variables.
Definition: codegen_neuron_cpp_visitor.cpp:1423
-
nmodl::codegen::CodegenNeuronCppVisitor::print_compute_functions
void print_compute_functions() override
Print all compute functions for every backend.
Definition: codegen_neuron_cpp_visitor.cpp:2041
-
nmodl::codegen::CodegenNeuronCppVisitor::print_thread_memory_callbacks
void print_thread_memory_callbacks()
Print thread variable (de-)initialization functions.
Definition: codegen_neuron_cpp_visitor.cpp:1258
-
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_cur_kernel
void print_nrn_cur_kernel(const ast::BreakpointBlock &node) override
Print main body of nrn_cur function.
Definition: codegen_neuron_cpp_visitor.cpp:1842
+
nmodl::codegen::CodegenNeuronCppVisitor::print_thread_variables_structure
void print_thread_variables_structure(bool print_initializers)
Print the data structure used to access thread variables.
Definition: codegen_neuron_cpp_visitor.cpp:1418
+
nmodl::codegen::CodegenNeuronCppVisitor::print_compute_functions
void print_compute_functions() override
Print all compute functions for every backend.
Definition: codegen_neuron_cpp_visitor.cpp:2047
+
nmodl::codegen::CodegenNeuronCppVisitor::print_thread_memory_callbacks
void print_thread_memory_callbacks()
Print thread variable (de-)initialization functions.
Definition: codegen_neuron_cpp_visitor.cpp:1253
+
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_cur_kernel
void print_nrn_cur_kernel(const ast::BreakpointBlock &node) override
Print main body of nrn_cur function.
Definition: codegen_neuron_cpp_visitor.cpp:1846
nmodl::codegen::CodegenNeuronCppVisitor::conc_write_statement
std::string conc_write_statement(const std::string &ion_name, const std::string &concentration, int index) override
Generate Function call statement for nrn_wrote_conc.
Definition: codegen_neuron_cpp_visitor.cpp:569
nmodl::codegen::CodegenNeuronCppVisitor::print_mechanism_register
void print_mechanism_register() override
Print the mechanism registration function.
Definition: codegen_neuron_cpp_visitor.cpp:1101
-
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_jacob
void print_nrn_jacob()
Print nrn_jacob function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1520
+
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_jacob
void print_nrn_jacob()
Print nrn_jacob function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1515
codegen_info.hpp
Various types to store code generation specific information.
-
nmodl::codegen::CodegenNeuronCppVisitor::print_fast_imem_calculation
void print_fast_imem_calculation() override
Print fast membrane current calculation code.
Definition: codegen_neuron_cpp_visitor.cpp:1875
-
nmodl::codegen::CodegenNeuronCppVisitor::print_data_structures
void print_data_structures(bool print_initializers) override
Print all classes.
Definition: codegen_neuron_cpp_visitor.cpp:2009
+
nmodl::codegen::CodegenNeuronCppVisitor::print_fast_imem_calculation
void print_fast_imem_calculation() override
Print fast membrane current calculation code.
Definition: codegen_neuron_cpp_visitor.cpp:1879
+
nmodl::codegen::CodegenNeuronCppVisitor::print_data_structures
void print_data_structures(bool print_initializers) override
Print all classes.
Definition: codegen_neuron_cpp_visitor.cpp:2015
nmodl::codegen::CodegenNeuronCppVisitor::print_sdlists_init
void print_sdlists_init(bool print_initializers) override
Definition: codegen_neuron_cpp_visitor.cpp:778
nmodl::codegen::CodegenNeuronCppVisitor::external_method_arguments
const std::string external_method_arguments() noexcept override
Arguments for external functions called from generated code.
Definition: codegen_neuron_cpp_visitor.cpp:490
nmodl::codegen::CodegenNeuronCppVisitor::py_function_name
std::string py_function_name(const std::string &function_or_procedure_name) const
In non POINT_PROCESS mechanisms all functions and procedures need a py <func_or_proc_name> to be avai...
Definition: codegen_neuron_cpp_visitor.cpp:541
nmodl::codegen::ThreadVariableInfo::offset
size_t offset
The global variables ahead of this one require offset doubles to store.
Definition: codegen_neuron_cpp_visitor.hpp:71
-
nmodl::codegen::CodegenNeuronCppVisitor::print_node_data_structure
void print_node_data_structure(bool print_initializers)
Print the structure that wraps all node variables required for the NMODL.
Definition: codegen_neuron_cpp_visitor.cpp:1390
+
nmodl::codegen::CodegenNeuronCppVisitor::print_node_data_structure
void print_node_data_structure(bool print_initializers)
Print the structure that wraps all node variables required for the NMODL.
Definition: codegen_neuron_cpp_visitor.cpp:1385
nmodl::codegen::CppObjectSpecifier::Inline
@ Inline
-
nmodl::codegen::CodegenNeuronCppVisitor::print_make_instance
void print_make_instance() const
Print make_*_instance.
Definition: codegen_neuron_cpp_visitor.cpp:1339
+
nmodl::codegen::CodegenNeuronCppVisitor::print_make_instance
void print_make_instance() const
Print make_*_instance.
Definition: codegen_neuron_cpp_visitor.cpp:1334
nmodl::codegen::CodegenNeuronCppVisitor::print_atomic_reduction_pragma
void print_atomic_reduction_pragma() override
Print atomic update pragma for reduction statements.
Definition: codegen_neuron_cpp_visitor.cpp:96
nmodl::codegen::CodegenNeuronCppVisitor::print_namespace_stop
void print_namespace_stop() override
Prints the end of the neuron namespace.
Definition: codegen_neuron_cpp_visitor.cpp:564
nmodl::codegen::CodegenNeuronCppVisitor::print_setdata_functions
void print_setdata_functions()
Print NEURON functions related to setting global variables of the mechanism.
Definition: codegen_neuron_cpp_visitor.cpp:203
-
nmodl::codegen::CodegenNeuronCppVisitor::print_mechanism_variables_macros
void print_mechanism_variables_macros()
Print mechanism variables' related macros.
Definition: codegen_neuron_cpp_visitor.cpp:1960
+
nmodl::codegen::CodegenNeuronCppVisitor::print_mechanism_variables_macros
void print_mechanism_variables_macros()
Print mechanism variables' related macros.
Definition: codegen_neuron_cpp_visitor.cpp:1966
nmodl::codegen::CodegenNeuronCppVisitor
Visitor for printing C++ code compatible with legacy api of NEURON
Definition: codegen_neuron_cpp_visitor.hpp:85
-
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_constructor
void print_nrn_constructor() override
Print nrn_constructor function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1554
+
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_constructor
void print_nrn_constructor() override
Print nrn_constructor function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1549
nmodl::codegen::CodegenNeuronCppVisitor::print_check_table_function_prototypes
void print_check_table_function_prototypes()
Print all check_* function declarations.
Definition: codegen_neuron_cpp_visitor.cpp:158
logger.hpp
Implement logger based on spdlog library.
nmodl::codegen::BlockType
BlockType
Helper to represent various block types.
Definition: codegen_cpp_visitor.hpp:56
nmodl::codegen::ThreadVariableInfo::index
size_t index
There index global variables ahead of this one.
Definition: codegen_neuron_cpp_visitor.hpp:66
-
nmodl::codegen::CodegenNeuronCppVisitor::print_headers_include
void print_headers_include() override
Print all includes.
Definition: codegen_neuron_cpp_visitor.cpp:1927
+
nmodl::codegen::CodegenNeuronCppVisitor::print_headers_include
void print_headers_include() override
Print all includes.
Definition: codegen_neuron_cpp_visitor.cpp:1931
nmodl::codegen::CodegenNeuronCppVisitor::external_method_parameters
const ParamVector external_method_parameters(bool table=false) noexcept override
Parameters for functions in generated code that are called back from external code.
Definition: codegen_neuron_cpp_visitor.cpp:496
nmodl::codegen::CodegenNeuronCppVisitor::print_function_or_procedure
void print_function_or_procedure(const ast::Block &node, const std::string &name, const std::unordered_set< CppObjectSpecifier > &specifiers={ CppObjectSpecifier::Inline}) override
Print nmodl function or procedure (common code)
Definition: codegen_neuron_cpp_visitor.cpp:264
nmodl::codegen::ThreadVariableInfo::symbol
const std::shared_ptr< symtab::Symbol > symbol
Definition: codegen_neuron_cpp_visitor.hpp:61
-
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_current
void print_nrn_current(const ast::BreakpointBlock &node) override
Print the nrn_current kernel.
Definition: codegen_neuron_cpp_visitor.cpp:1749
+
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_current
void print_nrn_current(const ast::BreakpointBlock &node) override
Print the nrn_current kernel.
Definition: codegen_neuron_cpp_visitor.cpp:1753
nmodl::codegen::CodegenNeuronCppVisitor::position_of_float_var
int position_of_float_var(const std::string &name) const override
Determine the position in the data array for a given float variable.
Definition: codegen_neuron_cpp_visitor.cpp:64
nmodl::codegen::CodegenNeuronCppVisitor::get_variable_name
std::string get_variable_name(const std::string &name, bool use_instance=true) const override
Determine variable name in the structure of mechanism properties.
Definition: codegen_neuron_cpp_visitor.cpp:660
nmodl::codegen::CodegenCppVisitor
Visitor for printing C++ code compatible with legacy api of CoreNEURON
Definition: codegen_cpp_visitor.hpp:196
-
nmodl::codegen::CodegenNeuronCppVisitor::print_make_node_data
void print_make_node_data() const
Print make_*_node_data.
Definition: codegen_neuron_cpp_visitor.cpp:1404
+
nmodl::codegen::CodegenNeuronCppVisitor::print_make_node_data
void print_make_node_data() const
Print make_*_node_data.
Definition: codegen_neuron_cpp_visitor.cpp:1399
nmodl::codegen::CodegenNeuronCppVisitor::simulator_name
std::string simulator_name() override
Name of the simulator the code was generated for.
Definition: codegen_neuron_cpp_visitor.cpp:44
nmodl::codegen::CodegenNeuronCppVisitor::print_function_procedure_helper
void print_function_procedure_helper(const ast::Block &node) override
Common helper function to help printing function or procedure blocks.
Definition: codegen_neuron_cpp_visitor.cpp:297
nmodl::codegen::CodegenNeuronCppVisitor::add_variable_point_process
void add_variable_point_process(std::vector< IndexVariableInfo > &variables) override
Add the variable point_process during get_int_variables.
Definition: codegen_neuron_cpp_visitor.cpp:462
nmodl::codegen::CodegenNeuronCppVisitor::nrn_thread_arguments
std::string nrn_thread_arguments() const override
Arguments for "_threadargs_" macro in neuron implementation.
Definition: codegen_neuron_cpp_visitor.cpp:503
nmodl::codegen::CodegenNeuronCppVisitor::print_net_receive_registration
void print_net_receive_registration()
Print code to register the call-back for the NET_RECEIVE block.
-
nmodl::codegen::CodegenNeuronCppVisitor::print_codegen_routines
void print_codegen_routines() override
Print entry point to code generation.
Definition: codegen_neuron_cpp_visitor.cpp:2058
+
nmodl::codegen::CodegenNeuronCppVisitor::print_codegen_routines
void print_codegen_routines() override
Print entry point to code generation.
Definition: codegen_neuron_cpp_visitor.cpp:2064
nmodl::codegen::CodegenNeuronCppVisitor::internal_method_parameters
ParamVector internal_method_parameters() override
Parameters for internally defined functions.
Definition: codegen_neuron_cpp_visitor.cpp:474
-
nmodl::codegen::CodegenNeuronCppVisitor::print_net_receive
void print_net_receive()
Print net_receive call-back.
Definition: codegen_neuron_cpp_visitor.cpp:2156
+
nmodl::codegen::CodegenNeuronCppVisitor::print_net_receive
void print_net_receive()
Print net_receive call-back.
Definition: codegen_neuron_cpp_visitor.cpp:2162
nmodl::codegen::CodegenNeuronCppVisitor::print_function_prototypes
void print_function_prototypes() override
Print function and procedures prototype declaration.
Definition: codegen_neuron_cpp_visitor.cpp:253
nmodl::codegen::CodegenNeuronCppVisitor::print_mechanism_global_var_structure
void print_mechanism_global_var_structure(bool print_initializers) override
Print the structure that wraps all global variables used in the NMODL.
Definition: codegen_neuron_cpp_visitor.cpp:827
-
nmodl::codegen::CodegenNeuronCppVisitor::print_global_macros
void print_global_macros()
Print NEURON global variable macros.
Definition: codegen_neuron_cpp_visitor.cpp:1943
+
nmodl::codegen::CodegenNeuronCppVisitor::print_global_macros
void print_global_macros()
Print NEURON global variable macros.
Definition: codegen_neuron_cpp_visitor.cpp:1949
nmodl::codegen::CodegenCppVisitor::ParamVector
std::vector< std::tuple< std::string, std::string, std::string, std::string > > ParamVector
A vector of parameters represented by a 4-tuple of strings:
Definition: codegen_cpp_visitor.hpp:266
ast_visitor.hpp
Concrete visitor for all AST classes.
diff --git a/doxygen/namespacenmodl_1_1codegen.html b/doxygen/namespacenmodl_1_1codegen.html index f19a6c994..fcea82992 100644 --- a/doxygen/namespacenmodl_1_1codegen.html +++ b/doxygen/namespacenmodl_1_1codegen.html @@ -315,7 +315,7 @@

x[id] = _args[1];

So, the R in AST needs to be renamed with _args[1].

-

Definition at line 2141 of file codegen_neuron_cpp_visitor.cpp.

+

Definition at line 2147 of file codegen_neuron_cpp_visitor.cpp.

diff --git a/doxygen/src_2codegen_2codegen__neuron__cpp__visitor_8cpp_source.html b/doxygen/src_2codegen_2codegen__neuron__cpp__visitor_8cpp_source.html index 4bc58c0b8..30f4fb7fd 100644 --- a/doxygen/src_2codegen_2codegen__neuron__cpp__visitor_8cpp_source.html +++ b/doxygen/src_2codegen_2codegen__neuron__cpp__visitor_8cpp_source.html @@ -1209,1123 +1209,1129 @@
1113  printer->add_newline();
1114  }
1115 
-
1116  if (info.diam_used) {
-
1117  printer->add_line("_morphology_sym = hoc_lookup(\"morphology\");");
-
1118  printer->add_newline();
-
1119  }
-
1120 
-
1121  for (const auto& ion: info.ions) {
-
1122  printer->fmt_line("_{0}_sym = hoc_lookup(\"{0}_ion\");", ion.name);
-
1123  }
-
1124  if (!info.ions.empty()) {
-
1125  printer->add_newline();
-
1126  }
-
1127 
-
1128  const auto compute_functions_parameters =
-
1129  breakpoint_exist()
-
1130  ? fmt::format("{}, {}, {}",
-
1131  nrn_cur_required() ? method_name(naming::NRN_CUR_METHOD) : "nullptr",
-
1132  method_name(naming::NRN_JACOB_METHOD),
-
1133  nrn_state_required() ? method_name(naming::NRN_STATE_METHOD) : "nullptr")
-
1134  : "nullptr, nullptr, nullptr";
-
1135  const auto register_mech_args = fmt::format("{}, {}, {}, {}, {}, {}",
-
1136  get_channel_info_var_name(),
-
1137  method_name(naming::NRN_ALLOC_METHOD),
-
1138  compute_functions_parameters,
-
1139  method_name(naming::NRN_INIT_METHOD),
-
1140  naming::NRN_POINTERINDEX,
-
1141  1 + info.thread_data_index);
-
1142  if (info.point_process) {
-
1143  printer->fmt_line(
-
1144  "_pointtype = point_register_mech({}, _hoc_create_pnt, _hoc_destroy_pnt, "
-
1145  "_member_func);",
-
1146  register_mech_args);
-
1147  } else {
-
1148  printer->fmt_line("register_mech({});", register_mech_args);
-
1149  }
-
1150 
-
1151  /// type related information
-
1152  printer->add_newline();
-
1153  printer->fmt_line("mech_type = nrn_get_mechtype({}[1]);", get_channel_info_var_name());
-
1154 
-
1155  // register the table-checking function
-
1156  if (info.table_count > 0) {
-
1157  printer->fmt_line("_nrn_thread_table_reg(mech_type, {});", table_thread_function_name());
-
1158  }
-
1159 
-
1160  /// Call _nrn_mechanism_register_data_fields() with the correct arguments
-
1161  /// Geenerated code follows the style underneath
+
1116  for (const auto& ion: info.ions) {
+
1117  printer->fmt_line("_{0}_sym = hoc_lookup(\"{0}_ion\");", ion.name);
+
1118  }
+
1119  if (!info.ions.empty()) {
+
1120  printer->add_newline();
+
1121  }
+
1122 
+
1123  const auto compute_functions_parameters =
+
1124  breakpoint_exist()
+
1125  ? fmt::format("{}, {}, {}",
+
1126  nrn_cur_required() ? method_name(naming::NRN_CUR_METHOD) : "nullptr",
+
1127  method_name(naming::NRN_JACOB_METHOD),
+
1128  nrn_state_required() ? method_name(naming::NRN_STATE_METHOD) : "nullptr")
+
1129  : "nullptr, nullptr, nullptr";
+
1130  const auto register_mech_args = fmt::format("{}, {}, {}, {}, {}, {}",
+
1131  get_channel_info_var_name(),
+
1132  method_name(naming::NRN_ALLOC_METHOD),
+
1133  compute_functions_parameters,
+
1134  method_name(naming::NRN_INIT_METHOD),
+
1135  naming::NRN_POINTERINDEX,
+
1136  1 + info.thread_data_index);
+
1137  if (info.point_process) {
+
1138  printer->fmt_line(
+
1139  "_pointtype = point_register_mech({}, _hoc_create_pnt, _hoc_destroy_pnt, "
+
1140  "_member_func);",
+
1141  register_mech_args);
+
1142  } else {
+
1143  printer->fmt_line("register_mech({});", register_mech_args);
+
1144  }
+
1145 
+
1146  /// type related information
+
1147  printer->add_newline();
+
1148  printer->fmt_line("mech_type = nrn_get_mechtype({}[1]);", get_channel_info_var_name());
+
1149 
+
1150  // register the table-checking function
+
1151  if (info.table_count > 0) {
+
1152  printer->fmt_line("_nrn_thread_table_reg(mech_type, {});", table_thread_function_name());
+
1153  }
+
1154 
+
1155  /// Call _nrn_mechanism_register_data_fields() with the correct arguments
+
1156  /// Geenerated code follows the style underneath
+
1157  ///
+
1158  /// _nrn_mechanism_register_data_fields(mech_type,
+
1159  /// _nrn_mechanism_field<double>{"var_name"}, /* float var index 0 */
+
1160  /// ...
+
1161  /// );
1162  ///
-
1163  /// _nrn_mechanism_register_data_fields(mech_type,
-
1164  /// _nrn_mechanism_field<double>{"var_name"}, /* float var index 0 */
-
1165  /// ...
-
1166  /// );
-
1167  ///
-
1168  /// TODO: More things to add here
-
1169  printer->add_line("_nrn_mechanism_register_data_fields(mech_type,");
-
1170  printer->increase_indent();
-
1171 
-
1172  const auto codegen_float_variables_size = codegen_float_variables.size();
-
1173  std::vector<std::string> mech_register_args;
-
1174 
-
1175  for (int i = 0; i < codegen_float_variables_size; ++i) {
-
1176  const auto& float_var = codegen_float_variables[i];
-
1177  if (float_var->is_array()) {
-
1178  mech_register_args.push_back(
-
1179  fmt::format("_nrn_mechanism_field<double>{{\"{}\", {}}} /* {} */",
-
1180  float_var->get_name(),
-
1181  float_var->get_length(),
-
1182  i));
-
1183  } else {
-
1184  mech_register_args.push_back(fmt::format(
-
1185  "_nrn_mechanism_field<double>{{\"{}\"}} /* {} */", float_var->get_name(), i));
-
1186  }
-
1187  }
-
1188 
-
1189  const auto codegen_int_variables_size = codegen_int_variables.size();
-
1190  for (int i = 0; i < codegen_int_variables_size; ++i) {
-
1191  const auto& int_var = codegen_int_variables[i];
-
1192  const auto& name = int_var.symbol->get_name();
-
1193  if (i != info.semantics[i].index) {
-
1194  throw std::runtime_error("Broken logic.");
-
1195  }
-
1196 
-
1197  auto type = "double*";
-
1198  if (name == naming::POINT_PROCESS_VARIABLE) {
-
1199  type = "Point_process*";
-
1200  } else if (name == naming::TQITEM_VARIABLE) {
-
1201  type = "void*";
-
1202  }
-
1203  mech_register_args.push_back(
-
1204  fmt::format("_nrn_mechanism_field<{}>{{\"{}\", \"{}\"}} /* {} */",
-
1205  type,
-
1206  name,
-
1207  info.semantics[i].name,
-
1208  i));
-
1209  }
-
1210  if (info.emit_cvode) {
-
1211  mech_register_args.push_back(
-
1212  "_nrn_mechanism_field<int>{\"_cvode_ieq\", \"cvodeieq\"} /* 0 */");
-
1213  }
-
1214 
-
1215  printer->add_multi_line(fmt::format("{}", fmt::join(mech_register_args, ",\n")));
+
1163  /// TODO: More things to add here
+
1164  printer->add_line("_nrn_mechanism_register_data_fields(mech_type,");
+
1165  printer->increase_indent();
+
1166 
+
1167  const auto codegen_float_variables_size = codegen_float_variables.size();
+
1168  std::vector<std::string> mech_register_args;
+
1169 
+
1170  for (int i = 0; i < codegen_float_variables_size; ++i) {
+
1171  const auto& float_var = codegen_float_variables[i];
+
1172  if (float_var->is_array()) {
+
1173  mech_register_args.push_back(
+
1174  fmt::format("_nrn_mechanism_field<double>{{\"{}\", {}}} /* {} */",
+
1175  float_var->get_name(),
+
1176  float_var->get_length(),
+
1177  i));
+
1178  } else {
+
1179  mech_register_args.push_back(fmt::format(
+
1180  "_nrn_mechanism_field<double>{{\"{}\"}} /* {} */", float_var->get_name(), i));
+
1181  }
+
1182  }
+
1183 
+
1184  const auto codegen_int_variables_size = codegen_int_variables.size();
+
1185  for (int i = 0; i < codegen_int_variables_size; ++i) {
+
1186  const auto& int_var = codegen_int_variables[i];
+
1187  const auto& name = int_var.symbol->get_name();
+
1188  if (i != info.semantics[i].index) {
+
1189  throw std::runtime_error("Broken logic.");
+
1190  }
+
1191 
+
1192  auto type = "double*";
+
1193  if (name == naming::POINT_PROCESS_VARIABLE) {
+
1194  type = "Point_process*";
+
1195  } else if (name == naming::TQITEM_VARIABLE) {
+
1196  type = "void*";
+
1197  }
+
1198  mech_register_args.push_back(
+
1199  fmt::format("_nrn_mechanism_field<{}>{{\"{}\", \"{}\"}} /* {} */",
+
1200  type,
+
1201  name,
+
1202  info.semantics[i].name,
+
1203  i));
+
1204  }
+
1205  if (info.emit_cvode) {
+
1206  mech_register_args.push_back(
+
1207  "_nrn_mechanism_field<int>{\"_cvode_ieq\", \"cvodeieq\"} /* 0 */");
+
1208  }
+
1209 
+
1210  printer->add_multi_line(fmt::format("{}", fmt::join(mech_register_args, ",\n")));
+
1211 
+
1212  printer->decrease_indent();
+
1213  printer->add_line(");");
+
1214  printer->add_newline();
+
1215 
1216 
-
1217  printer->decrease_indent();
-
1218  printer->add_line(");");
-
1219  printer->add_newline();
+
1217  printer->fmt_line("hoc_register_prop_size(mech_type, {}, {});",
+
1218  float_variables_size(),
+
1219  int_variables_size());
1220 
-
1221 
-
1222  printer->fmt_line("hoc_register_prop_size(mech_type, {}, {});",
-
1223  float_variables_size(),
-
1224  int_variables_size());
+
1221  for (int i = 0; i < codegen_int_variables_size; ++i) {
+
1222  if (i != info.semantics[i].index) {
+
1223  throw std::runtime_error("Broken logic.");
+
1224  }
1225 
-
1226  for (int i = 0; i < codegen_int_variables_size; ++i) {
-
1227  if (i != info.semantics[i].index) {
-
1228  throw std::runtime_error("Broken logic.");
-
1229  }
+
1226  printer->fmt_line("hoc_register_dparam_semantics(mech_type, {}, \"{}\");",
+
1227  i,
+
1228  info.semantics[i].name);
+
1229  }
1230 
-
1231  printer->fmt_line("hoc_register_dparam_semantics(mech_type, {}, \"{}\");",
-
1232  i,
-
1233  info.semantics[i].name);
-
1234  }
-
1235 
-
1236  if (info.artificial_cell) {
-
1237  printer->fmt_line("add_nrn_artcell(mech_type, {});", info.tqitem_index);
+
1231  if (info.artificial_cell) {
+
1232  printer->fmt_line("add_nrn_artcell(mech_type, {});", info.tqitem_index);
+
1233  }
+
1234 
+
1235  printer->add_line("hoc_register_var(hoc_scalar_double, hoc_vector_double, hoc_intfunc);");
+
1236  if (!info.point_process) {
+
1237  printer->add_line("hoc_register_npy_direct(mech_type, npy_direct_func_proc);");
1238  }
-
1239 
-
1240  printer->add_line("hoc_register_var(hoc_scalar_double, hoc_vector_double, hoc_intfunc);");
-
1241  if (!info.point_process) {
-
1242  printer->add_line("hoc_register_npy_direct(mech_type, npy_direct_func_proc);");
-
1243  }
-
1244  if (info.net_receive_node) {
-
1245  printer->fmt_line("pnt_receive[mech_type] = nrn_net_receive_{};", info.mod_suffix);
-
1246  printer->fmt_line("pnt_receive_size[mech_type] = {};", info.num_net_receive_parameters);
+
1239  if (info.net_receive_node) {
+
1240  printer->fmt_line("pnt_receive[mech_type] = nrn_net_receive_{};", info.mod_suffix);
+
1241  printer->fmt_line("pnt_receive_size[mech_type] = {};", info.num_net_receive_parameters);
+
1242  }
+
1243 
+
1244  if (info.thread_callback_register) {
+
1245  printer->add_line("_nrn_thread_reg(mech_type, 1, thread_mem_init);");
+
1246  printer->add_line("_nrn_thread_reg(mech_type, 0, thread_mem_cleanup);");
1247  }
1248 
-
1249  if (info.thread_callback_register) {
-
1250  printer->add_line("_nrn_thread_reg(mech_type, 1, thread_mem_init);");
-
1251  printer->add_line("_nrn_thread_reg(mech_type, 0, thread_mem_cleanup);");
-
1252  }
-
1253 
-
1254  printer->pop_block();
-
1255 }
-
1256 
+
1249  printer->pop_block();
+
1250 }
+
1251 
+
1252 
+
1253 void CodegenNeuronCppVisitor::print_thread_memory_callbacks() {
+
1254  if (!info.thread_callback_register) {
+
1255  return;
+
1256  }
1257 
-
1258 void CodegenNeuronCppVisitor::print_thread_memory_callbacks() {
-
1259  if (!info.thread_callback_register) {
-
1260  return;
-
1261  }
-
1262 
-
1263  auto static_thread_data = get_variable_name("thread_data", false);
-
1264  auto inuse = get_variable_name("thread_data_in_use", false);
-
1265  auto thread_data_index = info.thread_var_thread_id;
-
1266  printer->push_block("static void thread_mem_init(Datum* _thread) ");
-
1267  printer->push_block(fmt::format("if({})", inuse));
-
1268  printer->fmt_line("_thread[{}] = {{neuron::container::do_not_search, new double[{}]{{}}}};",
+
1258  auto static_thread_data = get_variable_name("thread_data", false);
+
1259  auto inuse = get_variable_name("thread_data_in_use", false);
+
1260  auto thread_data_index = info.thread_var_thread_id;
+
1261  printer->push_block("static void thread_mem_init(Datum* _thread) ");
+
1262  printer->push_block(fmt::format("if({})", inuse));
+
1263  printer->fmt_line("_thread[{}] = {{neuron::container::do_not_search, new double[{}]{{}}}};",
+
1264  thread_data_index,
+
1265  info.thread_var_data_size + info.top_local_thread_size);
+
1266  printer->pop_block();
+
1267  printer->push_block("else");
+
1268  printer->fmt_line("_thread[{}] = {{neuron::container::do_not_search, {}}};",
1269  thread_data_index,
-
1270  info.thread_var_data_size + info.top_local_thread_size);
-
1271  printer->pop_block();
-
1272  printer->push_block("else");
-
1273  printer->fmt_line("_thread[{}] = {{neuron::container::do_not_search, {}}};",
-
1274  thread_data_index,
-
1275  static_thread_data);
-
1276  printer->fmt_line("{} = 1;", inuse);
-
1277  printer->pop_block();
-
1278  printer->pop_block();
-
1279 
-
1280  printer->push_block("static void thread_mem_cleanup(Datum* _thread) ");
-
1281  printer->fmt_line("double * _thread_data_ptr = _thread[{}].get<double*>();", thread_data_index);
-
1282  printer->push_block(fmt::format("if(_thread_data_ptr == {})", static_thread_data));
-
1283  printer->fmt_line("{} = 0;", inuse);
-
1284  printer->pop_block();
-
1285  printer->push_block("else");
-
1286  printer->add_line("delete[] _thread_data_ptr;");
-
1287  printer->pop_block();
-
1288  printer->pop_block();
-
1289 }
-
1290 
-
1291 
-
1292 void CodegenNeuronCppVisitor::print_neuron_global_variable_declarations() {
-
1293  for (auto const& [var, type]: info.neuron_global_variables) {
-
1294  auto const name = var->get_name();
-
1295  printer->fmt_line("extern {} {};", type, name);
-
1296  }
-
1297 }
-
1298 
-
1299 void CodegenNeuronCppVisitor::print_mechanism_range_var_structure(bool print_initializers) {
-
1300  auto const value_initialize = print_initializers ? "{}" : "";
-
1301  auto int_type = default_int_data_type();
-
1302  printer->add_newline(2);
-
1303  printer->add_line("/** all mechanism instance variables and global variables */");
-
1304  printer->fmt_push_block("struct {} ", instance_struct());
-
1305 
-
1306  for (auto const& [var, type]: info.neuron_global_variables) {
-
1307  auto const name = var->get_name();
-
1308  printer->fmt_line("{}* {}{};",
-
1309  type,
-
1310  name,
-
1311  print_initializers ? fmt::format("{{&::{}}}", name) : std::string{});
-
1312  }
-
1313  for (auto& var: codegen_float_variables) {
-
1314  const auto& name = var->get_name();
-
1315  printer->fmt_line("double* {}{};", name, value_initialize);
-
1316  }
-
1317  for (auto& var: codegen_int_variables) {
-
1318  const auto& name = var.symbol->get_name();
-
1319  if (name == naming::POINT_PROCESS_VARIABLE) {
-
1320  continue;
-
1321  } else if (var.is_index || var.is_integer) {
-
1322  auto qualifier = var.is_constant ? "const " : "";
-
1323  printer->fmt_line("{}{}* const* {}{};", qualifier, int_type, name, value_initialize);
-
1324  } else {
-
1325  auto qualifier = var.is_constant ? "const " : "";
-
1326  auto type = var.is_vdata ? "void*" : default_float_data_type();
-
1327  printer->fmt_line("{}{}* const* {}{};", qualifier, type, name, value_initialize);
-
1328  }
-
1329  }
-
1330 
-
1331  printer->fmt_line("{}* {}{};",
-
1332  global_struct(),
-
1333  naming::INST_GLOBAL_MEMBER,
-
1334  print_initializers ? fmt::format("{{&{}}}", global_struct_instance())
-
1335  : std::string{});
-
1336  printer->pop_block(";");
-
1337 }
-
1338 
-
1339 void CodegenNeuronCppVisitor::print_make_instance() const {
-
1340  printer->add_newline(2);
-
1341  printer->fmt_push_block("static {} make_instance_{}(_nrn_mechanism_cache_range& _lmc)",
-
1342  instance_struct(),
-
1343  info.mod_suffix);
-
1344  printer->fmt_push_block("return {}", instance_struct());
-
1345 
-
1346  std::vector<std::string> make_instance_args;
-
1347 
+
1270  static_thread_data);
+
1271  printer->fmt_line("{} = 1;", inuse);
+
1272  printer->pop_block();
+
1273  printer->pop_block();
+
1274 
+
1275  printer->push_block("static void thread_mem_cleanup(Datum* _thread) ");
+
1276  printer->fmt_line("double * _thread_data_ptr = _thread[{}].get<double*>();", thread_data_index);
+
1277  printer->push_block(fmt::format("if(_thread_data_ptr == {})", static_thread_data));
+
1278  printer->fmt_line("{} = 0;", inuse);
+
1279  printer->pop_block();
+
1280  printer->push_block("else");
+
1281  printer->add_line("delete[] _thread_data_ptr;");
+
1282  printer->pop_block();
+
1283  printer->pop_block();
+
1284 }
+
1285 
+
1286 
+
1287 void CodegenNeuronCppVisitor::print_neuron_global_variable_declarations() {
+
1288  for (auto const& [var, type]: info.neuron_global_variables) {
+
1289  auto const name = var->get_name();
+
1290  printer->fmt_line("extern {} {};", type, name);
+
1291  }
+
1292 }
+
1293 
+
1294 void CodegenNeuronCppVisitor::print_mechanism_range_var_structure(bool print_initializers) {
+
1295  auto const value_initialize = print_initializers ? "{}" : "";
+
1296  auto int_type = default_int_data_type();
+
1297  printer->add_newline(2);
+
1298  printer->add_line("/** all mechanism instance variables and global variables */");
+
1299  printer->fmt_push_block("struct {} ", instance_struct());
+
1300 
+
1301  for (auto const& [var, type]: info.neuron_global_variables) {
+
1302  auto const name = var->get_name();
+
1303  printer->fmt_line("{}* {}{};",
+
1304  type,
+
1305  name,
+
1306  print_initializers ? fmt::format("{{&::{}}}", name) : std::string{});
+
1307  }
+
1308  for (auto& var: codegen_float_variables) {
+
1309  const auto& name = var->get_name();
+
1310  printer->fmt_line("double* {}{};", name, value_initialize);
+
1311  }
+
1312  for (auto& var: codegen_int_variables) {
+
1313  const auto& name = var.symbol->get_name();
+
1314  if (name == naming::POINT_PROCESS_VARIABLE) {
+
1315  continue;
+
1316  } else if (var.is_index || var.is_integer) {
+
1317  auto qualifier = var.is_constant ? "const " : "";
+
1318  printer->fmt_line("{}{}* const* {}{};", qualifier, int_type, name, value_initialize);
+
1319  } else {
+
1320  auto qualifier = var.is_constant ? "const " : "";
+
1321  auto type = var.is_vdata ? "void*" : default_float_data_type();
+
1322  printer->fmt_line("{}{}* const* {}{};", qualifier, type, name, value_initialize);
+
1323  }
+
1324  }
+
1325 
+
1326  printer->fmt_line("{}* {}{};",
+
1327  global_struct(),
+
1328  naming::INST_GLOBAL_MEMBER,
+
1329  print_initializers ? fmt::format("{{&{}}}", global_struct_instance())
+
1330  : std::string{});
+
1331  printer->pop_block(";");
+
1332 }
+
1333 
+
1334 void CodegenNeuronCppVisitor::print_make_instance() const {
+
1335  printer->add_newline(2);
+
1336  printer->fmt_push_block("static {} make_instance_{}(_nrn_mechanism_cache_range& _lmc)",
+
1337  instance_struct(),
+
1338  info.mod_suffix);
+
1339  printer->fmt_push_block("return {}", instance_struct());
+
1340 
+
1341  std::vector<std::string> make_instance_args;
+
1342 
+
1343 
+
1344  for (auto const& [var, type]: info.neuron_global_variables) {
+
1345  auto const name = var->get_name();
+
1346  make_instance_args.push_back(fmt::format("&::{}", name));
+
1347  }
1348 
-
1349  for (auto const& [var, type]: info.neuron_global_variables) {
-
1350  auto const name = var->get_name();
-
1351  make_instance_args.push_back(fmt::format("&::{}", name));
-
1352  }
-
1353 
-
1354 
-
1355  const auto codegen_float_variables_size = codegen_float_variables.size();
-
1356  for (int i = 0; i < codegen_float_variables_size; ++i) {
-
1357  const auto& float_var = codegen_float_variables[i];
-
1358  if (float_var->is_array()) {
-
1359  make_instance_args.push_back(
-
1360  fmt::format("_lmc.template data_array_ptr<{}, {}>()", i, float_var->get_length()));
-
1361  } else {
-
1362  make_instance_args.push_back(fmt::format("_lmc.template fpfield_ptr<{}>()", i));
-
1363  }
-
1364  }
-
1365 
-
1366  const auto codegen_int_variables_size = codegen_int_variables.size();
-
1367  for (size_t i = 0; i < codegen_int_variables_size; ++i) {
-
1368  const auto& var = codegen_int_variables[i];
-
1369  auto name = var.symbol->get_name();
-
1370  auto const variable = [&var, i]() -> std::string {
-
1371  if (var.is_index || var.is_integer) {
-
1372  return "";
-
1373  } else if (var.is_vdata) {
-
1374  return "";
-
1375  } else {
-
1376  return fmt::format("_lmc.template dptr_field_ptr<{}>()", i);
-
1377  }
-
1378  }();
-
1379  if (variable != "") {
-
1380  make_instance_args.push_back(variable);
-
1381  }
-
1382  }
-
1383 
-
1384  printer->add_multi_line(fmt::format("{}", fmt::join(make_instance_args, ",\n")));
-
1385 
-
1386  printer->pop_block(";");
-
1387  printer->pop_block();
-
1388 }
-
1389 
-
1390 void CodegenNeuronCppVisitor::print_node_data_structure(bool print_initializers) {
-
1391  printer->add_newline(2);
-
1392  printer->fmt_push_block("struct {} ", node_data_struct());
-
1393 
-
1394  // Pointers to node variables
-
1395  printer->add_line("int const * nodeindices;");
-
1396  printer->add_line("double const * node_voltages;");
-
1397  printer->add_line("double * node_diagonal;");
-
1398  printer->add_line("double * node_rhs;");
-
1399  printer->add_line("int nodecount;");
-
1400 
-
1401  printer->pop_block(";");
-
1402 }
-
1403 
-
1404 void CodegenNeuronCppVisitor::print_make_node_data() const {
-
1405  printer->add_newline(2);
-
1406  printer->fmt_push_block("static {} make_node_data_{}(NrnThread& nt, Memb_list& _ml_arg)",
-
1407  node_data_struct(),
-
1408  info.mod_suffix);
-
1409 
-
1410  std::vector<std::string> make_node_data_args = {"_ml_arg.nodeindices",
-
1411  "nt.node_voltage_storage()",
-
1412  "nt.node_d_storage()",
-
1413  "nt.node_rhs_storage()",
-
1414  "_ml_arg.nodecount"};
-
1415 
-
1416  printer->fmt_push_block("return {}", node_data_struct());
-
1417  printer->add_multi_line(fmt::format("{}", fmt::join(make_node_data_args, ",\n")));
-
1418 
-
1419  printer->pop_block(";");
-
1420  printer->pop_block();
-
1421 }
+
1349 
+
1350  const auto codegen_float_variables_size = codegen_float_variables.size();
+
1351  for (int i = 0; i < codegen_float_variables_size; ++i) {
+
1352  const auto& float_var = codegen_float_variables[i];
+
1353  if (float_var->is_array()) {
+
1354  make_instance_args.push_back(
+
1355  fmt::format("_lmc.template data_array_ptr<{}, {}>()", i, float_var->get_length()));
+
1356  } else {
+
1357  make_instance_args.push_back(fmt::format("_lmc.template fpfield_ptr<{}>()", i));
+
1358  }
+
1359  }
+
1360 
+
1361  const auto codegen_int_variables_size = codegen_int_variables.size();
+
1362  for (size_t i = 0; i < codegen_int_variables_size; ++i) {
+
1363  const auto& var = codegen_int_variables[i];
+
1364  auto name = var.symbol->get_name();
+
1365  auto const variable = [&var, i]() -> std::string {
+
1366  if (var.is_index || var.is_integer) {
+
1367  return "";
+
1368  } else if (var.is_vdata) {
+
1369  return "";
+
1370  } else {
+
1371  return fmt::format("_lmc.template dptr_field_ptr<{}>()", i);
+
1372  }
+
1373  }();
+
1374  if (variable != "") {
+
1375  make_instance_args.push_back(variable);
+
1376  }
+
1377  }
+
1378 
+
1379  printer->add_multi_line(fmt::format("{}", fmt::join(make_instance_args, ",\n")));
+
1380 
+
1381  printer->pop_block(";");
+
1382  printer->pop_block();
+
1383 }
+
1384 
+
1385 void CodegenNeuronCppVisitor::print_node_data_structure(bool print_initializers) {
+
1386  printer->add_newline(2);
+
1387  printer->fmt_push_block("struct {} ", node_data_struct());
+
1388 
+
1389  // Pointers to node variables
+
1390  printer->add_line("int const * nodeindices;");
+
1391  printer->add_line("double const * node_voltages;");
+
1392  printer->add_line("double * node_diagonal;");
+
1393  printer->add_line("double * node_rhs;");
+
1394  printer->add_line("int nodecount;");
+
1395 
+
1396  printer->pop_block(";");
+
1397 }
+
1398 
+
1399 void CodegenNeuronCppVisitor::print_make_node_data() const {
+
1400  printer->add_newline(2);
+
1401  printer->fmt_push_block("static {} make_node_data_{}(NrnThread& nt, Memb_list& _ml_arg)",
+
1402  node_data_struct(),
+
1403  info.mod_suffix);
+
1404 
+
1405  std::vector<std::string> make_node_data_args = {"_ml_arg.nodeindices",
+
1406  "nt.node_voltage_storage()",
+
1407  "nt.node_d_storage()",
+
1408  "nt.node_rhs_storage()",
+
1409  "_ml_arg.nodecount"};
+
1410 
+
1411  printer->fmt_push_block("return {}", node_data_struct());
+
1412  printer->add_multi_line(fmt::format("{}", fmt::join(make_node_data_args, ",\n")));
+
1413 
+
1414  printer->pop_block(";");
+
1415  printer->pop_block();
+
1416 }
+
1417 
+
1418 void CodegenNeuronCppVisitor::print_thread_variables_structure(bool print_initializers) {
+
1419  if (codegen_thread_variables.empty()) {
+
1420  return;
+
1421  }
1422 
-
1423 void CodegenNeuronCppVisitor::print_thread_variables_structure(bool print_initializers) {
-
1424  if (codegen_thread_variables.empty()) {
-
1425  return;
-
1426  }
+
1423  printer->add_newline(2);
+
1424  printer->fmt_push_block("struct {} ", thread_variables_struct());
+
1425  printer->add_line("double * thread_data;");
+
1426  printer->add_newline();
1427 
-
1428  printer->add_newline(2);
-
1429  printer->fmt_push_block("struct {} ", thread_variables_struct());
-
1430  printer->add_line("double * thread_data;");
-
1431  printer->add_newline();
-
1432 
-
1433  std::string simd_width = "1";
-
1434 
+
1428  std::string simd_width = "1";
+
1429 
+
1430 
+
1431  for (const auto& var_info: codegen_thread_variables) {
+
1432  printer->fmt_push_block("double * {}_ptr(size_t id)", var_info.symbol->get_name());
+
1433  printer->fmt_line("return thread_data + {} + (id % {});", var_info.offset, simd_width);
+
1434  printer->pop_block();
1435 
-
1436  for (const auto& var_info: codegen_thread_variables) {
-
1437  printer->fmt_push_block("double * {}_ptr(size_t id)", var_info.symbol->get_name());
-
1438  printer->fmt_line("return thread_data + {} + (id % {});", var_info.offset, simd_width);
-
1439  printer->pop_block();
-
1440 
-
1441  printer->fmt_push_block("double & {}(size_t id)", var_info.symbol->get_name());
-
1442  printer->fmt_line("return thread_data[{} + (id % {})];", var_info.offset, simd_width);
-
1443  printer->pop_block();
-
1444  }
-
1445  printer->add_newline();
-
1446 
-
1447  printer->push_block(fmt::format("{}(double * const thread_data)", thread_variables_struct()));
-
1448  printer->fmt_line("this->thread_data = thread_data;");
-
1449  printer->pop_block();
-
1450 
-
1451  printer->pop_block(";");
-
1452 }
-
1453 
-
1454 
-
1455 void CodegenNeuronCppVisitor::print_initial_block(const InitialBlock* node) {
-
1456  // read ion statements
-
1457  auto read_statements = ion_read_statements(BlockType::Initial);
-
1458  for (auto& statement: read_statements) {
-
1459  printer->add_line(statement);
-
1460  }
-
1461 
-
1462  // initial block
-
1463  if (node != nullptr) {
-
1464  const auto& block = node->get_statement_block();
-
1465  print_statement_block(*block, false, false);
-
1466  }
-
1467 
-
1468  // write ion statements
-
1469  auto write_statements = ion_write_statements(BlockType::Initial);
-
1470  for (auto& statement: write_statements) {
-
1471  auto text = process_shadow_update_statement(statement, BlockType::Initial);
-
1472  printer->add_line(text);
-
1473  }
-
1474 }
-
1475 
-
1476 
-
1477 void CodegenNeuronCppVisitor::print_global_function_common_code(BlockType type,
-
1478  const std::string& function_name) {
-
1479  std::string method = function_name.empty() ? compute_method_name(type) : function_name;
-
1480  ParamVector args = {{"", "const _nrn_model_sorted_token&", "", "_sorted_token"},
-
1481  {"", "NrnThread*", "", "nt"},
-
1482  {"", "Memb_list*", "", "_ml_arg"},
-
1483  {"", "int", "", "_type"}};
-
1484  printer->fmt_push_block("void {}({})", method, get_parameter_str(args));
-
1485 
-
1486  printer->add_line("_nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};");
-
1487  printer->fmt_line("auto inst = make_instance_{}(_lmc);", info.mod_suffix);
-
1488  printer->fmt_line("auto node_data = make_node_data_{}(*nt, *_ml_arg);", info.mod_suffix);
-
1489 
-
1490  printer->add_line("auto nodecount = _ml_arg->nodecount;");
-
1491  printer->add_line("auto* _thread = _ml_arg->_thread;");
-
1492  if (!codegen_thread_variables.empty()) {
-
1493  printer->fmt_line("auto _thread_vars = {}(_thread[{}].get<double*>());",
-
1494  thread_variables_struct(),
-
1495  info.thread_var_thread_id);
-
1496  }
-
1497 }
-
1498 
+
1436  printer->fmt_push_block("double & {}(size_t id)", var_info.symbol->get_name());
+
1437  printer->fmt_line("return thread_data[{} + (id % {})];", var_info.offset, simd_width);
+
1438  printer->pop_block();
+
1439  }
+
1440  printer->add_newline();
+
1441 
+
1442  printer->push_block(fmt::format("{}(double * const thread_data)", thread_variables_struct()));
+
1443  printer->fmt_line("this->thread_data = thread_data;");
+
1444  printer->pop_block();
+
1445 
+
1446  printer->pop_block(";");
+
1447 }
+
1448 
+
1449 
+
1450 void CodegenNeuronCppVisitor::print_initial_block(const InitialBlock* node) {
+
1451  // read ion statements
+
1452  auto read_statements = ion_read_statements(BlockType::Initial);
+
1453  for (auto& statement: read_statements) {
+
1454  printer->add_line(statement);
+
1455  }
+
1456 
+
1457  // initial block
+
1458  if (node != nullptr) {
+
1459  const auto& block = node->get_statement_block();
+
1460  print_statement_block(*block, false, false);
+
1461  }
+
1462 
+
1463  // write ion statements
+
1464  auto write_statements = ion_write_statements(BlockType::Initial);
+
1465  for (auto& statement: write_statements) {
+
1466  auto text = process_shadow_update_statement(statement, BlockType::Initial);
+
1467  printer->add_line(text);
+
1468  }
+
1469 }
+
1470 
+
1471 
+
1472 void CodegenNeuronCppVisitor::print_global_function_common_code(BlockType type,
+
1473  const std::string& function_name) {
+
1474  std::string method = function_name.empty() ? compute_method_name(type) : function_name;
+
1475  ParamVector args = {{"", "const _nrn_model_sorted_token&", "", "_sorted_token"},
+
1476  {"", "NrnThread*", "", "nt"},
+
1477  {"", "Memb_list*", "", "_ml_arg"},
+
1478  {"", "int", "", "_type"}};
+
1479  printer->fmt_push_block("void {}({})", method, get_parameter_str(args));
+
1480 
+
1481  printer->add_line("_nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};");
+
1482  printer->fmt_line("auto inst = make_instance_{}(_lmc);", info.mod_suffix);
+
1483  printer->fmt_line("auto node_data = make_node_data_{}(*nt, *_ml_arg);", info.mod_suffix);
+
1484 
+
1485  printer->add_line("auto nodecount = _ml_arg->nodecount;");
+
1486  printer->add_line("auto* _thread = _ml_arg->_thread;");
+
1487  if (!codegen_thread_variables.empty()) {
+
1488  printer->fmt_line("auto _thread_vars = {}(_thread[{}].get<double*>());",
+
1489  thread_variables_struct(),
+
1490  info.thread_var_thread_id);
+
1491  }
+
1492 }
+
1493 
+
1494 
+
1495 void CodegenNeuronCppVisitor::print_nrn_init(bool skip_init_check) {
+
1496  printer->add_newline(2);
+
1497 
+
1498  print_global_function_common_code(BlockType::Initial);
1499 
-
1500 void CodegenNeuronCppVisitor::print_nrn_init(bool skip_init_check) {
-
1501  printer->add_newline(2);
-
1502 
-
1503  print_global_function_common_code(BlockType::Initial);
-
1504 
-
1505  printer->push_block("for (int id = 0; id < nodecount; id++)");
-
1506 
-
1507  printer->add_line("auto* _ppvar = _ml_arg->pdata[id];");
-
1508  if (!info.artificial_cell) {
-
1509  printer->add_line("int node_id = node_data.nodeindices[id];");
-
1510  printer->add_line("auto v = node_data.node_voltages[node_id];");
-
1511  printer->fmt_line("inst.{}[id] = v;", naming::VOLTAGE_UNUSED_VARIABLE);
-
1512  }
-
1513 
-
1514  print_initial_block(info.initial_node);
-
1515  printer->pop_block();
-
1516 
-
1517  printer->pop_block();
-
1518 }
-
1519 
-
1520 void CodegenNeuronCppVisitor::print_nrn_jacob() {
-
1521  printer->add_newline(2);
+
1500  printer->push_block("for (int id = 0; id < nodecount; id++)");
+
1501 
+
1502  printer->add_line("auto* _ppvar = _ml_arg->pdata[id];");
+
1503  if (!info.artificial_cell) {
+
1504  printer->add_line("int node_id = node_data.nodeindices[id];");
+
1505  printer->add_line("auto v = node_data.node_voltages[node_id];");
+
1506  printer->fmt_line("inst.{}[id] = v;", naming::VOLTAGE_UNUSED_VARIABLE);
+
1507  }
+
1508 
+
1509  print_initial_block(info.initial_node);
+
1510  printer->pop_block();
+
1511 
+
1512  printer->pop_block();
+
1513 }
+
1514 
+
1515 void CodegenNeuronCppVisitor::print_nrn_jacob() {
+
1516  printer->add_newline(2);
+
1517 
+
1518  ParamVector args = {{"", "const _nrn_model_sorted_token&", "", "_sorted_token"},
+
1519  {"", "NrnThread*", "", "nt"},
+
1520  {"", "Memb_list*", "", "_ml_arg"},
+
1521  {"", "int", "", "_type"}};
1522 
-
1523  ParamVector args = {{"", "const _nrn_model_sorted_token&", "", "_sorted_token"},
-
1524  {"", "NrnThread*", "", "nt"},
-
1525  {"", "Memb_list*", "", "_ml_arg"},
-
1526  {"", "int", "", "_type"}};
+
1523  printer->fmt_push_block("static void {}({})",
+
1524  method_name(naming::NRN_JACOB_METHOD),
+
1525  get_parameter_str(args)); // begin function
+
1526 
1527 
-
1528  printer->fmt_push_block("static void {}({})",
-
1529  method_name(naming::NRN_JACOB_METHOD),
-
1530  get_parameter_str(args)); // begin function
-
1531 
-
1532 
-
1533  printer->add_multi_line(
-
1534  "_nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};");
+
1528  printer->add_multi_line(
+
1529  "_nrn_mechanism_cache_range _lmc{_sorted_token, *nt, *_ml_arg, _type};");
+
1530 
+
1531  printer->fmt_line("auto inst = make_instance_{}(_lmc);", info.mod_suffix);
+
1532  printer->fmt_line("auto node_data = make_node_data_{}(*nt, *_ml_arg);", info.mod_suffix);
+
1533  printer->fmt_line("auto nodecount = _ml_arg->nodecount;");
+
1534  printer->push_block("for (int id = 0; id < nodecount; id++)"); // begin for
1535 
-
1536  printer->fmt_line("auto inst = make_instance_{}(_lmc);", info.mod_suffix);
-
1537  printer->fmt_line("auto node_data = make_node_data_{}(*nt, *_ml_arg);", info.mod_suffix);
-
1538  printer->fmt_line("auto nodecount = _ml_arg->nodecount;");
-
1539  printer->push_block("for (int id = 0; id < nodecount; id++)"); // begin for
-
1540 
-
1541  if (breakpoint_exist()) {
-
1542  printer->add_line("int node_id = node_data.nodeindices[id];");
-
1543  printer->fmt_line("node_data.node_diagonal[node_id] += inst.{}[id];",
-
1544  info.vectorize ? naming::CONDUCTANCE_UNUSED_VARIABLE
-
1545  : naming::CONDUCTANCE_VARIABLE);
-
1546  }
-
1547 
-
1548  printer->pop_block(); // end for
-
1549  printer->pop_block(); // end function
-
1550 }
-
1551 
-
1552 
-
1553 /// TODO: Edit for NEURON
-
1554 void CodegenNeuronCppVisitor::print_nrn_constructor() {
-
1555  return;
-
1556 }
-
1557 
-
1558 
-
1559 /// TODO: Edit for NEURON
-
1560 void CodegenNeuronCppVisitor::print_nrn_destructor() {
-
1561  return;
-
1562 }
+
1536  if (breakpoint_exist()) {
+
1537  printer->add_line("int node_id = node_data.nodeindices[id];");
+
1538  printer->fmt_line("node_data.node_diagonal[node_id] += inst.{}[id];",
+
1539  info.vectorize ? naming::CONDUCTANCE_UNUSED_VARIABLE
+
1540  : naming::CONDUCTANCE_VARIABLE);
+
1541  }
+
1542 
+
1543  printer->pop_block(); // end for
+
1544  printer->pop_block(); // end function
+
1545 }
+
1546 
+
1547 
+
1548 /// TODO: Edit for NEURON
+
1549 void CodegenNeuronCppVisitor::print_nrn_constructor() {
+
1550  return;
+
1551 }
+
1552 
+
1553 
+
1554 /// TODO: Edit for NEURON
+
1555 void CodegenNeuronCppVisitor::print_nrn_destructor() {
+
1556  return;
+
1557 }
+
1558 
+
1559 
+
1560 /// TODO: Print the equivalent of `nrn_alloc_<mech_name>`
+
1561 void CodegenNeuronCppVisitor::print_nrn_alloc() {
+
1562  printer->add_newline(2);
1563 
-
1564 
-
1565 /// TODO: Print the equivalent of `nrn_alloc_<mech_name>`
-
1566 void CodegenNeuronCppVisitor::print_nrn_alloc() {
-
1567  printer->add_newline(2);
-
1568 
-
1569  auto method = method_name(naming::NRN_ALLOC_METHOD);
-
1570  printer->fmt_push_block("static void {}(Prop* _prop)", method);
-
1571  printer->add_multi_line(R"CODE(
-
1572  Prop *prop_ion{};
-
1573  Datum *_ppvar{};
-
1574  )CODE");
-
1575 
-
1576  if (info.point_process) {
-
1577  printer->push_block("if (nrn_point_prop_)");
-
1578  printer->add_multi_line(R"CODE(
-
1579  _nrn_mechanism_access_alloc_seq(_prop) = _nrn_mechanism_access_alloc_seq(nrn_point_prop_);
-
1580  _ppvar = _nrn_mechanism_access_dparam(nrn_point_prop_);
-
1581  )CODE");
-
1582  printer->chain_block("else");
+
1564  auto method = method_name(naming::NRN_ALLOC_METHOD);
+
1565  printer->fmt_push_block("static void {}(Prop* _prop)", method);
+
1566  printer->add_multi_line(R"CODE(
+
1567  Prop *prop_ion{};
+
1568  Datum *_ppvar{};
+
1569  )CODE");
+
1570 
+
1571  if (info.point_process) {
+
1572  printer->push_block("if (nrn_point_prop_)");
+
1573  printer->add_multi_line(R"CODE(
+
1574  _nrn_mechanism_access_alloc_seq(_prop) = _nrn_mechanism_access_alloc_seq(nrn_point_prop_);
+
1575  _ppvar = _nrn_mechanism_access_dparam(nrn_point_prop_);
+
1576  )CODE");
+
1577  printer->chain_block("else");
+
1578  }
+
1579  if (info.semantic_variable_count) {
+
1580  printer->fmt_line("_ppvar = nrn_prop_datum_alloc(mech_type, {}, _prop);",
+
1581  info.semantic_variable_count);
+
1582  printer->add_line("_nrn_mechanism_access_dparam(_prop) = _ppvar;");
1583  }
-
1584  if (info.semantic_variable_count) {
-
1585  printer->fmt_line("_ppvar = nrn_prop_datum_alloc(mech_type, {}, _prop);",
-
1586  info.semantic_variable_count);
-
1587  printer->add_line("_nrn_mechanism_access_dparam(_prop) = _ppvar;");
-
1588  }
-
1589  printer->add_multi_line(R"CODE(
-
1590  _nrn_mechanism_cache_instance _lmc{_prop};
-
1591  size_t const _iml{};
-
1592  )CODE");
-
1593  printer->fmt_line("assert(_nrn_mechanism_get_num_vars(_prop) == {});",
-
1594  codegen_float_variables.size());
-
1595  if (float_variables_size()) {
-
1596  printer->add_line("/*initialize range parameters*/");
-
1597  for (const auto& var: info.range_parameter_vars) {
-
1598  if (var->is_array()) {
-
1599  continue;
-
1600  }
-
1601  const auto& var_name = var->get_name();
-
1602  auto var_pos = position_of_float_var(var_name);
-
1603  double var_value = var->get_value() == nullptr ? 0.0 : *var->get_value();
-
1604 
-
1605  printer->fmt_line("_lmc.template fpfield<{}>(_iml) = {}; /* {} */",
-
1606  var_pos,
-
1607  var_value,
-
1608  var_name);
-
1609  }
-
1610  }
-
1611  if (info.point_process) {
-
1612  printer->pop_block();
-
1613  }
-
1614 
-
1615  if (info.semantic_variable_count) {
-
1616  printer->add_line("_nrn_mechanism_access_dparam(_prop) = _ppvar;");
-
1617  }
-
1618 
-
1619  if (info.diam_used) {
-
1620  throw std::runtime_error("Diam allocation not implemented.");
-
1621  }
+
1584  printer->add_multi_line(R"CODE(
+
1585  _nrn_mechanism_cache_instance _lmc{_prop};
+
1586  size_t const _iml{};
+
1587  )CODE");
+
1588  printer->fmt_line("assert(_nrn_mechanism_get_num_vars(_prop) == {});",
+
1589  codegen_float_variables.size());
+
1590  if (float_variables_size()) {
+
1591  printer->add_line("/*initialize range parameters*/");
+
1592  for (const auto& var: info.range_parameter_vars) {
+
1593  if (var->is_array()) {
+
1594  continue;
+
1595  }
+
1596  const auto& var_name = var->get_name();
+
1597  auto var_pos = position_of_float_var(var_name);
+
1598  double var_value = var->get_value() == nullptr ? 0.0 : *var->get_value();
+
1599 
+
1600  printer->fmt_line("_lmc.template fpfield<{}>(_iml) = {}; /* {} */",
+
1601  var_pos,
+
1602  var_value,
+
1603  var_name);
+
1604  }
+
1605  }
+
1606  if (info.point_process) {
+
1607  printer->pop_block();
+
1608  }
+
1609 
+
1610  if (info.semantic_variable_count) {
+
1611  printer->add_line("_nrn_mechanism_access_dparam(_prop) = _ppvar;");
+
1612  }
+
1613 
+
1614  const auto codegen_int_variables_size = codegen_int_variables.size();
+
1615 
+
1616  if (info.diam_used || info.area_used) {
+
1617  for (size_t i = 0; i < codegen_int_variables.size(); ++i) {
+
1618  auto var_info = codegen_int_variables[i];
+
1619  if (var_info.symbol->get_name() == naming::DIAM_VARIABLE) {
+
1620  printer->add_line("Symbol * morphology_sym = hoc_lookup(\"morphology\");");
+
1621  printer->fmt_line("Prop * morphology_prop = need_memb(morphology_sym);");
1622 
-
1623  if (info.area_used) {
-
1624  throw std::runtime_error("Area allocation not implemented.");
-
1625  }
-
1626 
-
1627  const auto codegen_int_variables_size = codegen_int_variables.size();
-
1628 
-
1629  for (const auto& ion: info.ions) {
-
1630  printer->fmt_line("Symbol * {}_sym = hoc_lookup(\"{}_ion\");", ion.name, ion.name);
-
1631  printer->fmt_line("Prop * {}_prop = need_memb({}_sym);", ion.name, ion.name);
+
1623  printer->fmt_line(
+
1624  "_ppvar[{}] = _nrn_mechanism_get_param_handle(morphology_prop, 0);", i);
+
1625  }
+
1626  if (var_info.symbol->get_name() == naming::AREA_VARIABLE) {
+
1627  printer->fmt_line("_ppvar[{}] = _nrn_mechanism_get_area_handle(nrn_alloc_node_);",
+
1628  i);
+
1629  }
+
1630  }
+
1631  }
1632 
-
1633  for (size_t i = 0; i < codegen_int_variables_size; ++i) {
-
1634  const auto& var = codegen_int_variables[i];
-
1635 
-
1636  // if(var.symbol->has_any_property(NmodlType::useion)) {
-
1637  const std::string& var_name = var.symbol->get_name();
-
1638  if (var_name.rfind("ion_", 0) != 0) {
-
1639  continue;
-
1640  }
-
1641 
-
1642  std::string ion_var_name = std::string(var_name.begin() + 4, var_name.end());
-
1643  if (ion.is_ionic_variable(ion_var_name)) {
-
1644  printer->fmt_line("_ppvar[{}] = _nrn_mechanism_get_param_handle({}_prop, {});",
-
1645  i,
-
1646  ion.name,
-
1647  ion.variable_index(ion_var_name));
-
1648  }
-
1649  // assign derivatives of the current as well
-
1650  else if (ion.is_current_derivative(ion_var_name)) {
-
1651  printer->fmt_line("_ppvar[{}] = _nrn_mechanism_get_param_handle({}_prop, {});",
-
1652  i,
-
1653  ion.name,
-
1654  ion.variable_index(ion_var_name));
-
1655  }
-
1656  //}
-
1657  }
-
1658  }
-
1659 
-
1660  /// TODO: CONSTRUCTOR call
-
1661 
-
1662  printer->pop_block();
-
1663 }
-
1664 
-
1665 
-
1666 /****************************************************************************************/
-
1667 /* Print nrn_state routine */
-
1668 /****************************************************************************************/
-
1669 
-
1670 /// TODO: Edit for NEURON
-
1671 void CodegenNeuronCppVisitor::print_nrn_state() {
-
1672  if (!nrn_state_required()) {
-
1673  return;
-
1674  }
-
1675 
-
1676  printer->add_newline(2);
-
1677  print_global_function_common_code(BlockType::State);
-
1678 
-
1679  printer->push_block("for (int id = 0; id < nodecount; id++)");
-
1680  printer->add_line("int node_id = node_data.nodeindices[id];");
-
1681  printer->add_line("auto* _ppvar = _ml_arg->pdata[id];");
-
1682  printer->add_line("auto v = node_data.node_voltages[node_id];");
-
1683 
-
1684  /**
-
1685  * \todo Eigen solver node also emits IonCurVar variable in the functor
-
1686  * but that shouldn't update ions in derivative block
-
1687  */
-
1688  if (ion_variable_struct_required()) {
-
1689  throw std::runtime_error("Not implemented.");
-
1690  }
-
1691 
-
1692  auto read_statements = ion_read_statements(BlockType::State);
-
1693  for (auto& statement: read_statements) {
-
1694  printer->add_line(statement);
-
1695  }
-
1696 
-
1697  if (info.nrn_state_block) {
-
1698  info.nrn_state_block->visit_children(*this);
+
1633  for (const auto& ion: info.ions) {
+
1634  printer->fmt_line("Symbol * {}_sym = hoc_lookup(\"{}_ion\");", ion.name, ion.name);
+
1635  printer->fmt_line("Prop * {}_prop = need_memb({}_sym);", ion.name, ion.name);
+
1636 
+
1637  for (size_t i = 0; i < codegen_int_variables_size; ++i) {
+
1638  const auto& var = codegen_int_variables[i];
+
1639 
+
1640  // if(var.symbol->has_any_property(NmodlType::useion)) {
+
1641  const std::string& var_name = var.symbol->get_name();
+
1642  if (var_name.rfind("ion_", 0) != 0) {
+
1643  continue;
+
1644  }
+
1645 
+
1646  std::string ion_var_name = std::string(var_name.begin() + 4, var_name.end());
+
1647  if (ion.is_ionic_variable(ion_var_name)) {
+
1648  printer->fmt_line("_ppvar[{}] = _nrn_mechanism_get_param_handle({}_prop, {});",
+
1649  i,
+
1650  ion.name,
+
1651  ion.variable_index(ion_var_name));
+
1652  }
+
1653  // assign derivatives of the current as well
+
1654  else if (ion.is_current_derivative(ion_var_name)) {
+
1655  printer->fmt_line("_ppvar[{}] = _nrn_mechanism_get_param_handle({}_prop, {});",
+
1656  i,
+
1657  ion.name,
+
1658  ion.variable_index(ion_var_name));
+
1659  }
+
1660  //}
+
1661  }
+
1662  }
+
1663 
+
1664  /// TODO: CONSTRUCTOR call
+
1665 
+
1666  printer->pop_block();
+
1667 }
+
1668 
+
1669 
+
1670 /****************************************************************************************/
+
1671 /* Print nrn_state routine */
+
1672 /****************************************************************************************/
+
1673 
+
1674 /// TODO: Edit for NEURON
+
1675 void CodegenNeuronCppVisitor::print_nrn_state() {
+
1676  if (!nrn_state_required()) {
+
1677  return;
+
1678  }
+
1679 
+
1680  printer->add_newline(2);
+
1681  print_global_function_common_code(BlockType::State);
+
1682 
+
1683  printer->push_block("for (int id = 0; id < nodecount; id++)");
+
1684  printer->add_line("int node_id = node_data.nodeindices[id];");
+
1685  printer->add_line("auto* _ppvar = _ml_arg->pdata[id];");
+
1686  printer->add_line("auto v = node_data.node_voltages[node_id];");
+
1687 
+
1688  /**
+
1689  * \todo Eigen solver node also emits IonCurVar variable in the functor
+
1690  * but that shouldn't update ions in derivative block
+
1691  */
+
1692  if (ion_variable_struct_required()) {
+
1693  throw std::runtime_error("Not implemented.");
+
1694  }
+
1695 
+
1696  auto read_statements = ion_read_statements(BlockType::State);
+
1697  for (auto& statement: read_statements) {
+
1698  printer->add_line(statement);
1699  }
1700 
-
1701  if (info.currents.empty() && info.breakpoint_node != nullptr) {
-
1702  auto block = info.breakpoint_node->get_statement_block();
-
1703  print_statement_block(*block, false, false);
-
1704  }
-
1705 
-
1706  const auto& write_statements = ion_write_statements(BlockType::State);
-
1707  for (auto& statement: write_statements) {
-
1708  const auto& text = process_shadow_update_statement(statement, BlockType::State);
-
1709  printer->add_line(text);
-
1710  }
-
1711 
-
1712  printer->pop_block();
-
1713  printer->pop_block();
-
1714 }
+
1701  if (info.nrn_state_block) {
+
1702  info.nrn_state_block->visit_children(*this);
+
1703  }
+
1704 
+
1705  if (info.currents.empty() && info.breakpoint_node != nullptr) {
+
1706  auto block = info.breakpoint_node->get_statement_block();
+
1707  print_statement_block(*block, false, false);
+
1708  }
+
1709 
+
1710  const auto& write_statements = ion_write_statements(BlockType::State);
+
1711  for (auto& statement: write_statements) {
+
1712  const auto& text = process_shadow_update_statement(statement, BlockType::State);
+
1713  printer->add_line(text);
+
1714  }
1715 
-
1716 
-
1717 /****************************************************************************************/
-
1718 /* Print nrn_cur related routines */
-
1719 /****************************************************************************************/
+
1716  printer->pop_block();
+
1717  printer->pop_block();
+
1718 }
+
1719 
1720 
-
1721 std::string CodegenNeuronCppVisitor::nrn_current_arguments() {
-
1722  return get_arg_str(nrn_current_parameters());
-
1723 }
+
1721 /****************************************************************************************/
+
1722 /* Print nrn_cur related routines */
+
1723 /****************************************************************************************/
1724 
-
1725 
-
1726 CodegenNeuronCppVisitor::ParamVector CodegenNeuronCppVisitor::nrn_current_parameters() {
-
1727  if (ion_variable_struct_required()) {
-
1728  throw std::runtime_error("Not implemented.");
-
1729  }
-
1730 
-
1731  ParamVector params = {{"", "_nrn_mechanism_cache_range&", "", "_lmc"},
-
1732  {"", "NrnThread*", "", "nt"},
-
1733  {"", "Datum*", "", "_ppvar"},
-
1734  {"", "Datum*", "", "_thread"}};
-
1735 
-
1736  if (info.thread_callback_register) {
-
1737  auto type_name = fmt::format("{}&", thread_variables_struct());
-
1738  params.emplace_back("", type_name, "", "_thread_vars");
-
1739  }
-
1740  params.emplace_back("", "size_t", "", "id");
-
1741  params.emplace_back("", fmt::format("{}&", instance_struct()), "", "inst");
-
1742  params.emplace_back("", fmt::format("{}&", node_data_struct()), "", "node_data");
-
1743  params.emplace_back("", "double", "", "v");
-
1744  return params;
-
1745 }
-
1746 
-
1747 
-
1748 /// TODO: Edit for NEURON
-
1749 void CodegenNeuronCppVisitor::print_nrn_current(const BreakpointBlock& node) {
-
1750  const auto& args = nrn_current_parameters();
-
1751  const auto& block = node.get_statement_block();
-
1752  printer->add_newline(2);
-
1753  printer->fmt_push_block("inline double nrn_current_{}({})",
-
1754  info.mod_suffix,
-
1755  get_parameter_str(args));
-
1756  printer->add_line("double current = 0.0;");
-
1757  print_statement_block(*block, false, false);
-
1758  for (auto& current: info.currents) {
-
1759  const auto& name = get_variable_name(current);
-
1760  printer->fmt_line("current += {};", name);
-
1761  }
-
1762  printer->add_line("return current;");
-
1763  printer->pop_block();
-
1764 }
-
1765 
-
1766 
-
1767 /// TODO: Edit for NEURON
-
1768 void CodegenNeuronCppVisitor::print_nrn_cur_conductance_kernel(const BreakpointBlock& node) {
-
1769  const auto& block = node.get_statement_block();
-
1770  print_statement_block(*block, false, false);
-
1771  if (!info.currents.empty()) {
-
1772  std::string sum;
-
1773  for (const auto& current: info.currents) {
-
1774  auto var = breakpoint_current(current);
-
1775  sum += get_variable_name(var);
-
1776  if (&current != &info.currents.back()) {
-
1777  sum += "+";
-
1778  }
-
1779  }
-
1780  printer->fmt_line("double rhs = {};", sum);
-
1781  }
-
1782 
-
1783  std::string sum;
-
1784  for (const auto& conductance: info.conductances) {
-
1785  auto var = breakpoint_current(conductance.variable);
-
1786  sum += get_variable_name(var);
-
1787  if (&conductance != &info.conductances.back()) {
-
1788  sum += "+";
-
1789  }
-
1790  }
-
1791  printer->fmt_line("double g = {};", sum);
-
1792 
-
1793  for (const auto& conductance: info.conductances) {
-
1794  if (!conductance.ion.empty()) {
-
1795  const auto& lhs = std::string(naming::ION_VARNAME_PREFIX) + "di" + conductance.ion +
-
1796  "dv";
-
1797  const auto& rhs = get_variable_name(conductance.variable);
-
1798  const ShadowUseStatement statement{lhs, "+=", rhs};
-
1799  const auto& text = process_shadow_update_statement(statement, BlockType::Equation);
-
1800  printer->add_line(text);
-
1801  }
-
1802  }
-
1803 }
-
1804 
-
1805 
-
1806 /// TODO: Edit for NEURON
-
1807 void CodegenNeuronCppVisitor::print_nrn_cur_non_conductance_kernel() {
-
1808  printer->fmt_line("double I1 = nrn_current_{}({}+0.001);",
-
1809  info.mod_suffix,
-
1810  nrn_current_arguments());
-
1811  for (auto& ion: info.ions) {
-
1812  for (auto& var: ion.writes) {
-
1813  if (ion.is_ionic_current(var)) {
-
1814  const auto& name = get_variable_name(var);
-
1815  printer->fmt_line("double di{} = {};", ion.name, name);
-
1816  }
-
1817  }
-
1818  }
-
1819  printer->fmt_line("double I0 = nrn_current_{}({});", info.mod_suffix, nrn_current_arguments());
-
1820  printer->add_line("double rhs = I0;");
-
1821 
-
1822  printer->add_line("double g = (I1-I0)/0.001;");
-
1823  for (auto& ion: info.ions) {
-
1824  for (auto& var: ion.writes) {
-
1825  if (ion.is_ionic_current(var)) {
-
1826  const auto& lhs = std::string(naming::ION_VARNAME_PREFIX) + "di" + ion.name + "dv";
-
1827  auto rhs = fmt::format("(di{}-{})/0.001", ion.name, get_variable_name(var));
-
1828  if (info.point_process) {
-
1829  auto area = get_variable_name(naming::NODE_AREA_VARIABLE);
-
1830  rhs += fmt::format("*1.e2/{}", area);
-
1831  }
-
1832  const ShadowUseStatement statement{lhs, "+=", rhs};
-
1833  const auto& text = process_shadow_update_statement(statement, BlockType::Equation);
-
1834  printer->add_line(text);
-
1835  }
-
1836  }
-
1837  }
-
1838 }
-
1839 
-
1840 
-
1841 /// TODO: Edit for NEURON
-
1842 void CodegenNeuronCppVisitor::print_nrn_cur_kernel(const BreakpointBlock& node) {
-
1843  printer->add_line("int node_id = node_data.nodeindices[id];");
-
1844  printer->add_line("double v = node_data.node_voltages[node_id];");
-
1845  printer->add_line("auto* _ppvar = _ml_arg->pdata[id];");
-
1846  const auto& read_statements = ion_read_statements(BlockType::Equation);
-
1847  for (auto& statement: read_statements) {
-
1848  printer->add_line(statement);
-
1849  }
-
1850 
-
1851  if (info.conductances.empty()) {
-
1852  print_nrn_cur_non_conductance_kernel();
-
1853  } else {
-
1854  print_nrn_cur_conductance_kernel(node);
-
1855  }
-
1856 
-
1857  const auto& write_statements = ion_write_statements(BlockType::Equation);
-
1858  for (auto& statement: write_statements) {
-
1859  auto text = process_shadow_update_statement(statement, BlockType::Equation);
-
1860  printer->add_line(text);
-
1861  }
-
1862 
-
1863  if (info.point_process) {
-
1864  const auto& area = get_variable_name(naming::NODE_AREA_VARIABLE);
-
1865  printer->fmt_line("double mfactor = 1.e2/{};", area);
-
1866  printer->add_line("g = g*mfactor;");
-
1867  printer->add_line("rhs = rhs*mfactor;");
-
1868  }
-
1869 
-
1870  // print_g_unused();
-
1871 }
-
1872 
-
1873 
-
1874 /// TODO: Edit for NEURON
-
1875 void CodegenNeuronCppVisitor::print_fast_imem_calculation() {
-
1876  return;
-
1877 }
-
1878 
-
1879 
-
1880 /// TODO: Edit for NEURON
-
1881 void CodegenNeuronCppVisitor::print_nrn_cur() {
-
1882  if (!nrn_cur_required()) {
-
1883  return;
-
1884  }
-
1885 
-
1886  if (info.conductances.empty()) {
-
1887  print_nrn_current(*info.breakpoint_node);
+
1725 std::string CodegenNeuronCppVisitor::nrn_current_arguments() {
+
1726  return get_arg_str(nrn_current_parameters());
+
1727 }
+
1728 
+
1729 
+
1730 CodegenNeuronCppVisitor::ParamVector CodegenNeuronCppVisitor::nrn_current_parameters() {
+
1731  if (ion_variable_struct_required()) {
+
1732  throw std::runtime_error("Not implemented.");
+
1733  }
+
1734 
+
1735  ParamVector params = {{"", "_nrn_mechanism_cache_range&", "", "_lmc"},
+
1736  {"", "NrnThread*", "", "nt"},
+
1737  {"", "Datum*", "", "_ppvar"},
+
1738  {"", "Datum*", "", "_thread"}};
+
1739 
+
1740  if (info.thread_callback_register) {
+
1741  auto type_name = fmt::format("{}&", thread_variables_struct());
+
1742  params.emplace_back("", type_name, "", "_thread_vars");
+
1743  }
+
1744  params.emplace_back("", "size_t", "", "id");
+
1745  params.emplace_back("", fmt::format("{}&", instance_struct()), "", "inst");
+
1746  params.emplace_back("", fmt::format("{}&", node_data_struct()), "", "node_data");
+
1747  params.emplace_back("", "double", "", "v");
+
1748  return params;
+
1749 }
+
1750 
+
1751 
+
1752 /// TODO: Edit for NEURON
+
1753 void CodegenNeuronCppVisitor::print_nrn_current(const BreakpointBlock& node) {
+
1754  const auto& args = nrn_current_parameters();
+
1755  const auto& block = node.get_statement_block();
+
1756  printer->add_newline(2);
+
1757  printer->fmt_push_block("inline double nrn_current_{}({})",
+
1758  info.mod_suffix,
+
1759  get_parameter_str(args));
+
1760  printer->add_line("double current = 0.0;");
+
1761  print_statement_block(*block, false, false);
+
1762  for (auto& current: info.currents) {
+
1763  const auto& name = get_variable_name(current);
+
1764  printer->fmt_line("current += {};", name);
+
1765  }
+
1766  printer->add_line("return current;");
+
1767  printer->pop_block();
+
1768 }
+
1769 
+
1770 
+
1771 /// TODO: Edit for NEURON
+
1772 void CodegenNeuronCppVisitor::print_nrn_cur_conductance_kernel(const BreakpointBlock& node) {
+
1773  const auto& block = node.get_statement_block();
+
1774  print_statement_block(*block, false, false);
+
1775  if (!info.currents.empty()) {
+
1776  std::string sum;
+
1777  for (const auto& current: info.currents) {
+
1778  auto var = breakpoint_current(current);
+
1779  sum += get_variable_name(var);
+
1780  if (&current != &info.currents.back()) {
+
1781  sum += "+";
+
1782  }
+
1783  }
+
1784  printer->fmt_line("double rhs = {};", sum);
+
1785  }
+
1786 
+
1787  std::string sum;
+
1788  for (const auto& conductance: info.conductances) {
+
1789  auto var = breakpoint_current(conductance.variable);
+
1790  sum += get_variable_name(var);
+
1791  if (&conductance != &info.conductances.back()) {
+
1792  sum += "+";
+
1793  }
+
1794  }
+
1795  printer->fmt_line("double g = {};", sum);
+
1796 
+
1797  for (const auto& conductance: info.conductances) {
+
1798  if (!conductance.ion.empty()) {
+
1799  const auto& lhs = std::string(naming::ION_VARNAME_PREFIX) + "di" + conductance.ion +
+
1800  "dv";
+
1801  const auto& rhs = get_variable_name(conductance.variable);
+
1802  const ShadowUseStatement statement{lhs, "+=", rhs};
+
1803  const auto& text = process_shadow_update_statement(statement, BlockType::Equation);
+
1804  printer->add_line(text);
+
1805  }
+
1806  }
+
1807 }
+
1808 
+
1809 
+
1810 /// TODO: Edit for NEURON
+
1811 void CodegenNeuronCppVisitor::print_nrn_cur_non_conductance_kernel() {
+
1812  printer->fmt_line("double I1 = nrn_current_{}({}+0.001);",
+
1813  info.mod_suffix,
+
1814  nrn_current_arguments());
+
1815  for (auto& ion: info.ions) {
+
1816  for (auto& var: ion.writes) {
+
1817  if (ion.is_ionic_current(var)) {
+
1818  const auto& name = get_variable_name(var);
+
1819  printer->fmt_line("double di{} = {};", ion.name, name);
+
1820  }
+
1821  }
+
1822  }
+
1823  printer->fmt_line("double I0 = nrn_current_{}({});", info.mod_suffix, nrn_current_arguments());
+
1824  printer->add_line("double rhs = I0;");
+
1825 
+
1826  printer->add_line("double g = (I1-I0)/0.001;");
+
1827  for (auto& ion: info.ions) {
+
1828  for (auto& var: ion.writes) {
+
1829  if (ion.is_ionic_current(var)) {
+
1830  const auto& lhs = std::string(naming::ION_VARNAME_PREFIX) + "di" + ion.name + "dv";
+
1831  auto rhs = fmt::format("(di{}-{})/0.001", ion.name, get_variable_name(var));
+
1832  if (info.point_process) {
+
1833  auto area = get_variable_name(naming::NODE_AREA_VARIABLE);
+
1834  rhs += fmt::format("*1.e2/{}", area);
+
1835  }
+
1836  const ShadowUseStatement statement{lhs, "+=", rhs};
+
1837  const auto& text = process_shadow_update_statement(statement, BlockType::Equation);
+
1838  printer->add_line(text);
+
1839  }
+
1840  }
+
1841  }
+
1842 }
+
1843 
+
1844 
+
1845 /// TODO: Edit for NEURON
+
1846 void CodegenNeuronCppVisitor::print_nrn_cur_kernel(const BreakpointBlock& node) {
+
1847  printer->add_line("int node_id = node_data.nodeindices[id];");
+
1848  printer->add_line("double v = node_data.node_voltages[node_id];");
+
1849  printer->add_line("auto* _ppvar = _ml_arg->pdata[id];");
+
1850  const auto& read_statements = ion_read_statements(BlockType::Equation);
+
1851  for (auto& statement: read_statements) {
+
1852  printer->add_line(statement);
+
1853  }
+
1854 
+
1855  if (info.conductances.empty()) {
+
1856  print_nrn_cur_non_conductance_kernel();
+
1857  } else {
+
1858  print_nrn_cur_conductance_kernel(node);
+
1859  }
+
1860 
+
1861  const auto& write_statements = ion_write_statements(BlockType::Equation);
+
1862  for (auto& statement: write_statements) {
+
1863  auto text = process_shadow_update_statement(statement, BlockType::Equation);
+
1864  printer->add_line(text);
+
1865  }
+
1866 
+
1867  if (info.point_process) {
+
1868  const auto& area = get_variable_name(naming::NODE_AREA_VARIABLE);
+
1869  printer->fmt_line("double mfactor = 1.e2/{};", area);
+
1870  printer->add_line("g = g*mfactor;");
+
1871  printer->add_line("rhs = rhs*mfactor;");
+
1872  }
+
1873 
+
1874  // print_g_unused();
+
1875 }
+
1876 
+
1877 
+
1878 /// TODO: Edit for NEURON
+
1879 void CodegenNeuronCppVisitor::print_fast_imem_calculation() {
+
1880  return;
+
1881 }
+
1882 
+
1883 
+
1884 /// TODO: Edit for NEURON
+
1885 void CodegenNeuronCppVisitor::print_nrn_cur() {
+
1886  if (!nrn_cur_required()) {
+
1887  return;
1888  }
1889 
-
1890  printer->add_newline(2);
-
1891  printer->add_line("/** update current */");
-
1892  print_global_function_common_code(BlockType::Equation);
-
1893  // print_channel_iteration_block_parallel_hint(BlockType::Equation, info.breakpoint_node);
-
1894  printer->push_block("for (int id = 0; id < nodecount; id++)");
-
1895  print_nrn_cur_kernel(*info.breakpoint_node);
-
1896  // print_nrn_cur_matrix_shadow_update();
-
1897  // if (!nrn_cur_reduction_loop_required()) {
-
1898  // print_fast_imem_calculation();
-
1899  // }
-
1900 
-
1901 
-
1902  printer->add_line("node_data.node_rhs[node_id] -= rhs;");
-
1903 
-
1904  if (breakpoint_exist()) {
-
1905  printer->fmt_line("inst.{}[id] = g;",
-
1906  info.vectorize ? naming::CONDUCTANCE_UNUSED_VARIABLE
-
1907  : naming::CONDUCTANCE_VARIABLE);
-
1908  }
-
1909  printer->pop_block();
-
1910 
-
1911  // if (nrn_cur_reduction_loop_required()) {
-
1912  // printer->push_block("for (int id = 0; id < nodecount; id++)");
-
1913  // print_nrn_cur_matrix_shadow_reduction();
-
1914  // printer->pop_block();
-
1915  // print_fast_imem_calculation();
-
1916  // }
-
1917 
-
1918  // print_kernel_data_present_annotation_block_end();
-
1919  printer->pop_block();
-
1920 }
+
1890  if (info.conductances.empty()) {
+
1891  print_nrn_current(*info.breakpoint_node);
+
1892  }
+
1893 
+
1894  printer->add_newline(2);
+
1895  printer->add_line("/** update current */");
+
1896  print_global_function_common_code(BlockType::Equation);
+
1897  // print_channel_iteration_block_parallel_hint(BlockType::Equation, info.breakpoint_node);
+
1898  printer->push_block("for (int id = 0; id < nodecount; id++)");
+
1899  print_nrn_cur_kernel(*info.breakpoint_node);
+
1900  // print_nrn_cur_matrix_shadow_update();
+
1901  // if (!nrn_cur_reduction_loop_required()) {
+
1902  // print_fast_imem_calculation();
+
1903  // }
+
1904 
+
1905 
+
1906  printer->add_line("node_data.node_rhs[node_id] -= rhs;");
+
1907 
+
1908  if (breakpoint_exist()) {
+
1909  printer->fmt_line("inst.{}[id] = g;",
+
1910  info.vectorize ? naming::CONDUCTANCE_UNUSED_VARIABLE
+
1911  : naming::CONDUCTANCE_VARIABLE);
+
1912  }
+
1913  printer->pop_block();
+
1914 
+
1915  // if (nrn_cur_reduction_loop_required()) {
+
1916  // printer->push_block("for (int id = 0; id < nodecount; id++)");
+
1917  // print_nrn_cur_matrix_shadow_reduction();
+
1918  // printer->pop_block();
+
1919  // print_fast_imem_calculation();
+
1920  // }
1921 
-
1922 
-
1923 /****************************************************************************************/
-
1924 /* Main code printing entry points */
-
1925 /****************************************************************************************/
+
1922  // print_kernel_data_present_annotation_block_end();
+
1923  printer->pop_block();
+
1924 }
+
1925 
1926 
-
1927 void CodegenNeuronCppVisitor::print_headers_include() {
-
1928  print_standard_includes();
-
1929  print_neuron_includes();
+
1927 /****************************************************************************************/
+
1928 /* Main code printing entry points */
+
1929 /****************************************************************************************/
1930 
-
1931  if (info.thread_callback_register) {
-
1932  printer->add_line("extern void _nrn_thread_reg(int, int, void(*)(Datum*));");
-
1933  }
-
1934 }
-
1935 
-
1936 
-
1937 void CodegenNeuronCppVisitor::print_macro_definitions() {
-
1938  print_global_macros();
-
1939  print_mechanism_variables_macros();
-
1940 }
-
1941 
-
1942 
-
1943 void CodegenNeuronCppVisitor::print_global_macros() {
-
1944  printer->add_newline();
-
1945  printer->add_line("/* NEURON global macro definitions */");
-
1946  if (info.vectorize) {
-
1947  printer->add_multi_line(R"CODE(
-
1948  /* VECTORIZED */
-
1949  #define NRN_VECTORIZED 1
-
1950  )CODE");
-
1951  } else {
-
1952  printer->add_multi_line(R"CODE(
-
1953  /* NOT VECTORIZED */
-
1954  #define NRN_VECTORIZED 0
-
1955  )CODE");
-
1956  }
-
1957 }
-
1958 
-
1959 
-
1960 void CodegenNeuronCppVisitor::print_mechanism_variables_macros() {
-
1961  printer->add_newline();
-
1962  printer->add_line("static constexpr auto number_of_datum_variables = ",
-
1963  std::to_string(int_variables_size()),
-
1964  ";");
-
1965  printer->add_line("static constexpr auto number_of_floating_point_variables = ",
-
1966  std::to_string(codegen_float_variables.size()),
-
1967  ";");
-
1968  printer->add_newline();
-
1969  printer->add_multi_line(R"CODE(
-
1970  namespace {
-
1971  template <typename T>
-
1972  using _nrn_mechanism_std_vector = std::vector<T>;
-
1973  using _nrn_model_sorted_token = neuron::model_sorted_token;
-
1974  using _nrn_mechanism_cache_range = neuron::cache::MechanismRange<number_of_floating_point_variables, number_of_datum_variables>;
-
1975  using _nrn_mechanism_cache_instance = neuron::cache::MechanismInstance<number_of_floating_point_variables, number_of_datum_variables>;
-
1976  using _nrn_non_owning_id_without_container = neuron::container::non_owning_identifier_without_container;
+
1931 void CodegenNeuronCppVisitor::print_headers_include() {
+
1932  print_standard_includes();
+
1933  print_neuron_includes();
+
1934 
+
1935  if (info.thread_callback_register) {
+
1936  printer->add_line("extern void _nrn_thread_reg(int, int, void(*)(Datum*));");
+
1937  }
+
1938 }
+
1939 
+
1940 
+
1941 void CodegenNeuronCppVisitor::print_macro_definitions() {
+
1942  print_global_macros();
+
1943  print_mechanism_variables_macros();
+
1944 
+
1945  printer->add_line("extern Node* nrn_alloc_node_;");
+
1946 }
+
1947 
+
1948 
+
1949 void CodegenNeuronCppVisitor::print_global_macros() {
+
1950  printer->add_newline();
+
1951  printer->add_line("/* NEURON global macro definitions */");
+
1952  if (info.vectorize) {
+
1953  printer->add_multi_line(R"CODE(
+
1954  /* VECTORIZED */
+
1955  #define NRN_VECTORIZED 1
+
1956  )CODE");
+
1957  } else {
+
1958  printer->add_multi_line(R"CODE(
+
1959  /* NOT VECTORIZED */
+
1960  #define NRN_VECTORIZED 0
+
1961  )CODE");
+
1962  }
+
1963 }
+
1964 
+
1965 
+
1966 void CodegenNeuronCppVisitor::print_mechanism_variables_macros() {
+
1967  printer->add_newline();
+
1968  printer->add_line("static constexpr auto number_of_datum_variables = ",
+
1969  std::to_string(int_variables_size()),
+
1970  ";");
+
1971  printer->add_line("static constexpr auto number_of_floating_point_variables = ",
+
1972  std::to_string(codegen_float_variables.size()),
+
1973  ";");
+
1974  printer->add_newline();
+
1975  printer->add_multi_line(R"CODE(
+
1976  namespace {
1977  template <typename T>
-
1978  using _nrn_mechanism_field = neuron::mechanism::field<T>;
-
1979  template <typename... Args>
-
1980  void _nrn_mechanism_register_data_fields(Args&&... args) {
-
1981  neuron::mechanism::register_data_fields(std::forward<Args>(args)...);
-
1982  }
-
1983  } // namespace
-
1984  )CODE");
-
1985 
-
1986  if (info.point_process) {
-
1987  printer->add_line("extern Prop* nrn_point_prop_;");
-
1988  } else {
-
1989  printer->add_line("Prop* hoc_getdata_range(int type);");
-
1990  }
-
1991  /// TODO: More prints here?
-
1992  // for registration of tables
-
1993  if (info.table_count > 0) {
-
1994  printer->add_line("void _nrn_thread_table_reg(int, nrn_thread_table_check_t);");
-
1995  }
-
1996 }
-
1997 
-
1998 
-
1999 void CodegenNeuronCppVisitor::print_namespace_begin() {
-
2000  print_namespace_start();
-
2001 }
-
2002 
+
1978  using _nrn_mechanism_std_vector = std::vector<T>;
+
1979  using _nrn_model_sorted_token = neuron::model_sorted_token;
+
1980  using _nrn_mechanism_cache_range = neuron::cache::MechanismRange<number_of_floating_point_variables, number_of_datum_variables>;
+
1981  using _nrn_mechanism_cache_instance = neuron::cache::MechanismInstance<number_of_floating_point_variables, number_of_datum_variables>;
+
1982  using _nrn_non_owning_id_without_container = neuron::container::non_owning_identifier_without_container;
+
1983  template <typename T>
+
1984  using _nrn_mechanism_field = neuron::mechanism::field<T>;
+
1985  template <typename... Args>
+
1986  void _nrn_mechanism_register_data_fields(Args&&... args) {
+
1987  neuron::mechanism::register_data_fields(std::forward<Args>(args)...);
+
1988  }
+
1989  } // namespace
+
1990  )CODE");
+
1991 
+
1992  if (info.point_process) {
+
1993  printer->add_line("extern Prop* nrn_point_prop_;");
+
1994  } else {
+
1995  printer->add_line("Prop* hoc_getdata_range(int type);");
+
1996  }
+
1997  /// TODO: More prints here?
+
1998  // for registration of tables
+
1999  if (info.table_count > 0) {
+
2000  printer->add_line("void _nrn_thread_table_reg(int, nrn_thread_table_check_t);");
+
2001  }
+
2002 }
2003 
-
2004 void CodegenNeuronCppVisitor::print_namespace_end() {
-
2005  print_namespace_stop();
-
2006 }
-
2007 
+
2004 
+
2005 void CodegenNeuronCppVisitor::print_namespace_begin() {
+
2006  print_namespace_start();
+
2007 }
2008 
-
2009 void CodegenNeuronCppVisitor::print_data_structures(bool print_initializers) {
-
2010  print_mechanism_global_var_structure(print_initializers);
-
2011  print_mechanism_range_var_structure(print_initializers);
-
2012  print_node_data_structure(print_initializers);
-
2013  print_thread_variables_structure(print_initializers);
-
2014  print_make_instance();
-
2015  print_make_node_data();
-
2016 }
-
2017 
-
2018 
-
2019 void CodegenNeuronCppVisitor::print_v_unused() const {
-
2020  if (!info.vectorize) {
-
2021  return;
-
2022  }
-
2023  printer->add_multi_line(R"CODE(
-
2024  #if NRN_PRCELLSTATE
-
2025  inst->v_unused[id] = v;
-
2026  #endif
-
2027  )CODE");
-
2028 }
-
2029 
-
2030 
-
2031 void CodegenNeuronCppVisitor::print_g_unused() const {
-
2032  printer->add_multi_line(R"CODE(
-
2033  #if NRN_PRCELLSTATE
-
2034  inst->g_unused[id] = g;
-
2035  #endif
-
2036  )CODE");
-
2037 }
-
2038 
-
2039 
-
2040 /// TODO: Edit for NEURON
-
2041 void CodegenNeuronCppVisitor::print_compute_functions() {
-
2042  print_hoc_py_wrapper_function_definitions();
-
2043  for (const auto& procedure: info.procedures) {
-
2044  print_procedure(*procedure);
-
2045  }
-
2046  for (const auto& function: info.functions) {
-
2047  print_function(*function);
-
2048  }
-
2049  print_nrn_init();
-
2050  print_nrn_cur();
-
2051  print_nrn_state();
-
2052  print_nrn_jacob();
-
2053  print_net_receive();
-
2054 }
-
2055 
-
2056 
-
2057 /// TODO: Edit for NEURON
-
2058 void CodegenNeuronCppVisitor::print_codegen_routines() {
-
2059  print_backend_info();
-
2060  print_headers_include();
-
2061  print_macro_definitions();
-
2062  print_neuron_global_variable_declarations();
-
2063  print_namespace_begin();
-
2064  print_nmodl_constants();
-
2065  print_prcellstate_macros();
-
2066  print_mechanism_info();
-
2067  print_data_structures(true);
-
2068  print_nrn_alloc();
-
2069  print_function_prototypes();
-
2070  print_functors_definitions();
-
2071  print_global_variables_for_hoc();
-
2072  print_thread_memory_callbacks();
-
2073  print_compute_functions(); // only nrn_cur and nrn_state
-
2074  print_sdlists_init(true);
-
2075  print_mechanism_register();
-
2076  print_namespace_end();
-
2077 }
-
2078 
-
2079 void CodegenNeuronCppVisitor::print_ion_variable() {
-
2080  throw std::runtime_error("Not implemented.");
-
2081 }
-
2082 
-
2083 
-
2084 void CodegenNeuronCppVisitor::print_net_send_call(const ast::FunctionCall& node) {
-
2085  auto const& arguments = node.get_arguments();
-
2086 
-
2087  if (printing_net_init) {
-
2088  throw std::runtime_error("Not implemented. [jfiwoei]");
-
2089  }
-
2090 
-
2091  std::string weight_pointer = "nullptr";
-
2092  auto point_process = get_variable_name(naming::POINT_PROCESS_VARIABLE,
-
2093  /* use_instance */ false);
-
2094  if (!printing_net_receive) {
-
2095  point_process += ".get<Point_process*>()";
-
2096  }
-
2097  const auto& tqitem = get_variable_name("tqitem", /* use_instance */ false);
-
2098 
-
2099  printer->fmt_text("net_send(/* tqitem */ &{}, {}, {}, {} + ",
-
2100  tqitem,
-
2101  weight_pointer,
-
2102  point_process,
-
2103  get_variable_name("t"));
-
2104  print_vector_elements(arguments, ", ");
-
2105  printer->add_text(')');
-
2106 }
-
2107 
-
2108 void CodegenNeuronCppVisitor::print_net_move_call(const ast::FunctionCall& node) {
-
2109  const auto& point_process = get_variable_name("point_process", /* use_instance */ false);
-
2110  const auto& tqitem = get_variable_name("tqitem", /* use_instance */ false);
-
2111 
-
2112  printer->fmt_text("net_move(/* tqitem */ &{}, {}, ", tqitem, point_process);
+
2009 
+
2010 void CodegenNeuronCppVisitor::print_namespace_end() {
+
2011  print_namespace_stop();
+
2012 }
+
2013 
+
2014 
+
2015 void CodegenNeuronCppVisitor::print_data_structures(bool print_initializers) {
+
2016  print_mechanism_global_var_structure(print_initializers);
+
2017  print_mechanism_range_var_structure(print_initializers);
+
2018  print_node_data_structure(print_initializers);
+
2019  print_thread_variables_structure(print_initializers);
+
2020  print_make_instance();
+
2021  print_make_node_data();
+
2022 }
+
2023 
+
2024 
+
2025 void CodegenNeuronCppVisitor::print_v_unused() const {
+
2026  if (!info.vectorize) {
+
2027  return;
+
2028  }
+
2029  printer->add_multi_line(R"CODE(
+
2030  #if NRN_PRCELLSTATE
+
2031  inst->v_unused[id] = v;
+
2032  #endif
+
2033  )CODE");
+
2034 }
+
2035 
+
2036 
+
2037 void CodegenNeuronCppVisitor::print_g_unused() const {
+
2038  printer->add_multi_line(R"CODE(
+
2039  #if NRN_PRCELLSTATE
+
2040  inst->g_unused[id] = g;
+
2041  #endif
+
2042  )CODE");
+
2043 }
+
2044 
+
2045 
+
2046 /// TODO: Edit for NEURON
+
2047 void CodegenNeuronCppVisitor::print_compute_functions() {
+
2048  print_hoc_py_wrapper_function_definitions();
+
2049  for (const auto& procedure: info.procedures) {
+
2050  print_procedure(*procedure);
+
2051  }
+
2052  for (const auto& function: info.functions) {
+
2053  print_function(*function);
+
2054  }
+
2055  print_nrn_init();
+
2056  print_nrn_cur();
+
2057  print_nrn_state();
+
2058  print_nrn_jacob();
+
2059  print_net_receive();
+
2060 }
+
2061 
+
2062 
+
2063 /// TODO: Edit for NEURON
+
2064 void CodegenNeuronCppVisitor::print_codegen_routines() {
+
2065  print_backend_info();
+
2066  print_headers_include();
+
2067  print_macro_definitions();
+
2068  print_neuron_global_variable_declarations();
+
2069  print_namespace_begin();
+
2070  print_nmodl_constants();
+
2071  print_prcellstate_macros();
+
2072  print_mechanism_info();
+
2073  print_data_structures(true);
+
2074  print_nrn_alloc();
+
2075  print_function_prototypes();
+
2076  print_functors_definitions();
+
2077  print_global_variables_for_hoc();
+
2078  print_thread_memory_callbacks();
+
2079  print_compute_functions(); // only nrn_cur and nrn_state
+
2080  print_sdlists_init(true);
+
2081  print_mechanism_register();
+
2082  print_namespace_end();
+
2083 }
+
2084 
+
2085 void CodegenNeuronCppVisitor::print_ion_variable() {
+
2086  throw std::runtime_error("Not implemented.");
+
2087 }
+
2088 
+
2089 
+
2090 void CodegenNeuronCppVisitor::print_net_send_call(const ast::FunctionCall& node) {
+
2091  auto const& arguments = node.get_arguments();
+
2092 
+
2093  if (printing_net_init) {
+
2094  throw std::runtime_error("Not implemented. [jfiwoei]");
+
2095  }
+
2096 
+
2097  std::string weight_pointer = "nullptr";
+
2098  auto point_process = get_variable_name(naming::POINT_PROCESS_VARIABLE,
+
2099  /* use_instance */ false);
+
2100  if (!printing_net_receive) {
+
2101  point_process += ".get<Point_process*>()";
+
2102  }
+
2103  const auto& tqitem = get_variable_name("tqitem", /* use_instance */ false);
+
2104 
+
2105  printer->fmt_text("net_send(/* tqitem */ &{}, {}, {}, {} + ",
+
2106  tqitem,
+
2107  weight_pointer,
+
2108  point_process,
+
2109  get_variable_name("t"));
+
2110  print_vector_elements(arguments, ", ");
+
2111  printer->add_text(')');
+
2112 }
2113 
-
2114  print_vector_elements(node.get_arguments(), ", ");
-
2115  printer->add_text(')');
-
2116 }
+
2114 void CodegenNeuronCppVisitor::print_net_move_call(const ast::FunctionCall& node) {
+
2115  const auto& point_process = get_variable_name("point_process", /* use_instance */ false);
+
2116  const auto& tqitem = get_variable_name("tqitem", /* use_instance */ false);
2117 
-
2118 void CodegenNeuronCppVisitor::print_net_event_call(const ast::FunctionCall& node) {
-
2119  const auto& point_process = get_variable_name(naming::POINT_PROCESS_VARIABLE,
-
2120  /* use_instance */ false);
-
2121  printer->fmt_text("net_event({}, t)", point_process);
+
2118  printer->fmt_text("net_move(/* tqitem */ &{}, {}, ", tqitem, point_process);
+
2119 
+
2120  print_vector_elements(node.get_arguments(), ", ");
+
2121  printer->add_text(')');
2122 }
-
2123 
-
2124 /**
-
2125  * Rename arguments to NET_RECEIVE block with corresponding pointer variable
-
2126  *
-
2127  * \code{.mod}
-
2128  * NET_RECEIVE (weight, R){
-
2129  * x = R
-
2130  * }
-
2131  * \endcode
+
2123 
+
2124 void CodegenNeuronCppVisitor::print_net_event_call(const ast::FunctionCall& node) {
+
2125  const auto& point_process = get_variable_name(naming::POINT_PROCESS_VARIABLE,
+
2126  /* use_instance */ false);
+
2127  printer->fmt_text("net_event({}, t)", point_process);
+
2128 }
+
2129 
+
2130 /**
+
2131  * Rename arguments to NET_RECEIVE block with corresponding pointer variable
2132  *
-
2133  * then generated code should be:
-
2134  *
-
2135  * \code{.cpp}
-
2136  * x[id] = _args[1];
+
2133  * \code{.mod}
+
2134  * NET_RECEIVE (weight, R){
+
2135  * x = R
+
2136  * }
2137  * \endcode
2138  *
-
2139  * So, the `R` in AST needs to be renamed with `_args[1]`.
-
2140  */
-
2141 static void rename_net_receive_arguments(const ast::NetReceiveBlock& net_receive_node,
-
2142  const ast::Node& node) {
-
2143  const auto& parameters = net_receive_node.get_parameters();
-
2144 
-
2145  auto n_parameters = parameters.size();
-
2146  for (size_t i = 0; i < n_parameters; ++i) {
-
2147  const auto& name = parameters[i]->get_node_name();
-
2148  auto var_used = VarUsageVisitor().variable_used(node, name);
-
2149  if (var_used) {
-
2150  RenameVisitor vr(name, fmt::format("_args[{}]", i));
-
2151  node.get_statement_block()->visit_children(vr);
-
2152  }
-
2153  }
-
2154 }
-
2155 
-
2156 void CodegenNeuronCppVisitor::print_net_receive() {
-
2157  printing_net_receive = true;
-
2158  auto node = info.net_receive_node;
-
2159  if (!node) {
-
2160  return;
-
2161  }
-
2162 
-
2163  ParamVector args = {{"", "Point_process*", "", "_pnt"},
-
2164  {"", "double*", "", "_args"},
-
2165  {"", "double", "", "flag"}};
-
2166 
-
2167  printer->fmt_push_block("static void nrn_net_receive_{}({})",
-
2168  info.mod_suffix,
-
2169  get_parameter_str(args));
-
2170 
-
2171  rename_net_receive_arguments(*node, *node);
+
2139  * then generated code should be:
+
2140  *
+
2141  * \code{.cpp}
+
2142  * x[id] = _args[1];
+
2143  * \endcode
+
2144  *
+
2145  * So, the `R` in AST needs to be renamed with `_args[1]`.
+
2146  */
+
2147 static void rename_net_receive_arguments(const ast::NetReceiveBlock& net_receive_node,
+
2148  const ast::Node& node) {
+
2149  const auto& parameters = net_receive_node.get_parameters();
+
2150 
+
2151  auto n_parameters = parameters.size();
+
2152  for (size_t i = 0; i < n_parameters; ++i) {
+
2153  const auto& name = parameters[i]->get_node_name();
+
2154  auto var_used = VarUsageVisitor().variable_used(node, name);
+
2155  if (var_used) {
+
2156  RenameVisitor vr(name, fmt::format("_args[{}]", i));
+
2157  node.get_statement_block()->visit_children(vr);
+
2158  }
+
2159  }
+
2160 }
+
2161 
+
2162 void CodegenNeuronCppVisitor::print_net_receive() {
+
2163  printing_net_receive = true;
+
2164  auto node = info.net_receive_node;
+
2165  if (!node) {
+
2166  return;
+
2167  }
+
2168 
+
2169  ParamVector args = {{"", "Point_process*", "", "_pnt"},
+
2170  {"", "double*", "", "_args"},
+
2171  {"", "double", "", "flag"}};
2172 
-
2173  printer->add_line("_nrn_mechanism_cache_instance _lmc{_pnt->prop};");
-
2174  printer->add_line("auto * nt = static_cast<NrnThread*>(_pnt->_vnt);");
-
2175  printer->add_line("auto * _ppvar = _nrn_mechanism_access_dparam(_pnt->prop);");
+
2173  printer->fmt_push_block("static void nrn_net_receive_{}({})",
+
2174  info.mod_suffix,
+
2175  get_parameter_str(args));
2176 
-
2177  printer->fmt_line("auto inst = make_instance_{}(_lmc);", info.mod_suffix);
-
2178  printer->fmt_line("// nocmodl has a nullptr dereference for thread variables.");
-
2179  printer->fmt_line("// NMODL will fail to compile at a later point, because of");
-
2180  printer->fmt_line("// missing '_thread_vars'.");
-
2181  printer->fmt_line("Datum * _thread = nullptr;");
+
2177  rename_net_receive_arguments(*node, *node);
+
2178 
+
2179  printer->add_line("_nrn_mechanism_cache_instance _lmc{_pnt->prop};");
+
2180  printer->add_line("auto * nt = static_cast<NrnThread*>(_pnt->_vnt);");
+
2181  printer->add_line("auto * _ppvar = _nrn_mechanism_access_dparam(_pnt->prop);");
2182 
-
2183  printer->add_line("size_t id = 0;");
-
2184  printer->add_line("double t = nt->_t;");
-
2185 
-
2186  print_statement_block(*node->get_statement_block(), false, false);
-
2187 
-
2188  printer->add_newline();
-
2189  printer->pop_block();
-
2190  printing_net_receive = false;
-
2191 }
-
2192 
+
2183  printer->fmt_line("auto inst = make_instance_{}(_lmc);", info.mod_suffix);
+
2184  printer->fmt_line("// nocmodl has a nullptr dereference for thread variables.");
+
2185  printer->fmt_line("// NMODL will fail to compile at a later point, because of");
+
2186  printer->fmt_line("// missing '_thread_vars'.");
+
2187  printer->fmt_line("Datum * _thread = nullptr;");
+
2188 
+
2189  printer->add_line("size_t id = 0;");
+
2190  printer->add_line("double t = nt->_t;");
+
2191 
+
2192  print_statement_block(*node->get_statement_block(), false, false);
2193 
-
2194 /****************************************************************************************/
-
2195 /* Overloaded visitor routines */
-
2196 /****************************************************************************************/
-
2197 
-
2198 /// TODO: Edit for NEURON
-
2199 void CodegenNeuronCppVisitor::visit_watch_statement(const ast::WatchStatement& /* node */) {
-
2200  return;
-
2201 }
-
2202 
-
2203 
-
2204 } // namespace codegen
-
2205 } // namespace nmodl
+
2194  printer->add_newline();
+
2195  printer->pop_block();
+
2196  printing_net_receive = false;
+
2197 }
+
2198 
+
2199 
+
2200 /****************************************************************************************/
+
2201 /* Overloaded visitor routines */
+
2202 /****************************************************************************************/
+
2203 
+
2204 /// TODO: Edit for NEURON
+
2205 void CodegenNeuronCppVisitor::visit_watch_statement(const ast::WatchStatement& /* node */) {
+
2206  return;
+
2207 }
+
2208 
+
2209 
+
2210 } // namespace codegen
+
2211 } // namespace nmodl
-
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_destructor
void print_nrn_destructor() override
Print nrn_destructor function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1560
+
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_destructor
void print_nrn_destructor() override
Print nrn_destructor function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1555
nmodl::ast::Node
Base class for all AST node.
Definition: node.hpp:40
nmodl::codegen::IndexVariableInfo::is_index
bool is_index
if this is pure index (e.g.
Definition: codegen_cpp_visitor.hpp:137
-
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_cur_non_conductance_kernel
void print_nrn_cur_non_conductance_kernel() override
Print the nrn_cur kernel without NMODL conductance keyword provisions.
Definition: codegen_neuron_cpp_visitor.cpp:1807
+
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_cur_non_conductance_kernel
void print_nrn_cur_non_conductance_kernel() override
Print the nrn_cur kernel without NMODL conductance keyword provisions.
Definition: codegen_neuron_cpp_visitor.cpp:1811
nmodl::codegen::CodegenNeuronCppVisitor::py_function_signature
std::string py_function_signature(const std::string &function_or_procedure_name) const
Get the signature of the npy <func_or_proc_name> function.
Definition: codegen_neuron_cpp_visitor.cpp:547
nmodl::codegen::IndexVariableInfo
Helper to represent information about index/int variables.
Definition: codegen_cpp_visitor.hpp:127
-
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_cur
void print_nrn_cur() override
Print nrn_cur / current update function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1881
-
nmodl::codegen::CodegenNeuronCppVisitor::print_macro_definitions
void print_macro_definitions()
Print all NEURON macros.
Definition: codegen_neuron_cpp_visitor.cpp:1937
+
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_cur
void print_nrn_cur() override
Print nrn_cur / current update function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1885
+
nmodl::codegen::CodegenNeuronCppVisitor::print_macro_definitions
void print_macro_definitions()
Print all NEURON macros.
Definition: codegen_neuron_cpp_visitor.cpp:1941
-
nmodl::codegen::CodegenNeuronCppVisitor::print_net_event_call
void print_net_event_call(const ast::FunctionCall &node) override
Print call to net_event.
Definition: codegen_neuron_cpp_visitor.cpp:2118
+
nmodl::codegen::CodegenNeuronCppVisitor::print_net_event_call
void print_net_event_call(const ast::FunctionCall &node) override
Print call to net_event.
Definition: codegen_neuron_cpp_visitor.cpp:2124
nmodl::codegen::naming::POINT_PROCESS_VARIABLE
static constexpr char POINT_PROCESS_VARIABLE[]
inbuilt neuron variable for point process
Definition: codegen_naming.hpp:63
nmodl::codegen::CodegenNeuronCppVisitor::print_neuron_includes
void print_neuron_includes()
Print includes from NEURON.
Definition: codegen_neuron_cpp_visitor.cpp:767
nmodl::codegen::naming::NRN_JACOB_METHOD
static constexpr char NRN_JACOB_METHOD[]
nrn_jacob method in generated code
Definition: codegen_naming.hpp:159
-
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_init
void print_nrn_init(bool skip_init_check=true)
Print the nrn_init function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1500
+
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_init
void print_nrn_init(bool skip_init_check=true)
Print the nrn_init function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1495
nmodl::codegen::CodegenNeuronCppVisitor::print_hoc_py_wrapper_function_body
void print_hoc_py_wrapper_function_body(const ast::Block *function_or_procedure_block, InterpreterWrapper wrapper_type)
Definition: codegen_neuron_cpp_visitor.cpp:336
nmodl::codegen::CodegenNeuronCppVisitor::internal_method_arguments
std::string internal_method_arguments() override
Arguments for functions that are defined and used internally.
Definition: codegen_neuron_cpp_visitor.cpp:468
nmodl::codegen::CodegenCppVisitor::SymbolType
std::shared_ptr< symtab::Symbol > SymbolType
Definition: codegen_cpp_visitor.hpp:254
-
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_alloc
void print_nrn_alloc() override
Print nrn_alloc function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1566
+
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_alloc
void print_nrn_alloc() override
Print nrn_alloc function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1561
nmodl::codegen::naming::VOLTAGE_UNUSED_VARIABLE
static constexpr char VOLTAGE_UNUSED_VARIABLE[]
range variable for voltage when unused (for vectorized model)
Definition: codegen_naming.hpp:78
nmodl::codegen::CodegenNeuronCppVisitor::register_mechanism_arguments
std::string register_mechanism_arguments() const override
Arguments for register_mech or point_register_mech function.
Definition: codegen_neuron_cpp_visitor.cpp:521
nmodl::codegen::CodegenNeuronCppVisitor::position_of_int_var
int position_of_int_var(const std::string &name) const override
Determine the position in the data array for a given int variable.
Definition: codegen_neuron_cpp_visitor.cpp:76
nmodl::ast::NetReceiveBlock::get_parameters
const ArgumentVector & get_parameters() const noexcept override
Getter for member variable NetReceiveBlock::parameters.
Definition: net_receive_block.hpp:176
- +
nmodl::codegen::CodegenNeuronCppVisitor::table_thread_function_name
std::string table_thread_function_name() const
Name of the threaded table checking function.
Definition: codegen_neuron_cpp_visitor.cpp:54
nmodl::codegen::CodegenNeuronCppVisitor::optimize_ion_variable_copies
bool optimize_ion_variable_copies() const override
Check if ion variable copies should be avoided.
Definition: codegen_neuron_cpp_visitor.cpp:100
nmodl::codegen::CodegenNeuronCppVisitor::hoc_function_name
std::string hoc_function_name(const std::string &function_or_procedure_name) const
All functions and procedures need a hoc <func_or_proc_name> to be available to the HOC interpreter.
Definition: codegen_neuron_cpp_visitor.cpp:526
@@ -2336,30 +2342,30 @@
codegen_neuron_cpp_visitor.hpp
Visitor for printing C++ code compatible with legacy api of NEURON
nmodl::codegen::CodegenNeuronCppVisitor::backend_name
std::string backend_name() const override
Name of the code generation backend.
Definition: codegen_neuron_cpp_visitor.cpp:49
nmodl::codegen::CodegenNeuronCppVisitor::process_verbatim_text
std::string process_verbatim_text(std::string const &text) override
Process a verbatim block for possible variable renaming.
Definition: codegen_neuron_cpp_visitor.cpp:515
- +
nmodl::codegen::naming::NTHREAD_DT_VARIABLE
static constexpr char NTHREAD_DT_VARIABLE[]
dt variable in neuron thread structure
Definition: codegen_naming.hpp:99
-
nmodl::codegen::CodegenNeuronCppVisitor::print_g_unused
void print_g_unused() const override
Set g_unused (conductance) for NRN_PRCELLSTATE feature.
Definition: codegen_neuron_cpp_visitor.cpp:2031
-
nmodl::codegen::CodegenNeuronCppVisitor::visit_watch_statement
void visit_watch_statement(const ast::WatchStatement &node) override
TODO: Edit for NEURON.
Definition: codegen_neuron_cpp_visitor.cpp:2199
+
nmodl::codegen::CodegenNeuronCppVisitor::print_g_unused
void print_g_unused() const override
Set g_unused (conductance) for NRN_PRCELLSTATE feature.
Definition: codegen_neuron_cpp_visitor.cpp:2037
+
nmodl::codegen::CodegenNeuronCppVisitor::visit_watch_statement
void visit_watch_statement(const ast::WatchStatement &node) override
TODO: Edit for NEURON.
Definition: codegen_neuron_cpp_visitor.cpp:2205
nmodl::ast::Ast::is_procedure_block
virtual bool is_procedure_block() const noexcept
Check if the ast node is an instance of ast::ProcedureBlock.
Definition: ast.cpp:144
-
nmodl::codegen::CodegenNeuronCppVisitor::print_net_send_call
void print_net_send_call(const ast::FunctionCall &node) override
Print call to net_send.
Definition: codegen_neuron_cpp_visitor.cpp:2084
+
nmodl::codegen::CodegenNeuronCppVisitor::print_net_send_call
void print_net_send_call(const ast::FunctionCall &node) override
Print call to net_send.
Definition: codegen_neuron_cpp_visitor.cpp:2090
var_usage_visitor.hpp
Check if variable is used in given block.
string_utils.hpp
Implement string manipulation functions.
-
nmodl::codegen::CodegenNeuronCppVisitor::print_namespace_end
void print_namespace_end() override
Print end of namespaces.
Definition: codegen_neuron_cpp_visitor.cpp:2004
-
nmodl::codegen::CodegenNeuronCppVisitor::print_net_move_call
void print_net_move_call(const ast::FunctionCall &node) override
Print call to net_move.
Definition: codegen_neuron_cpp_visitor.cpp:2108
+
nmodl::codegen::CodegenNeuronCppVisitor::print_namespace_end
void print_namespace_end() override
Print end of namespaces.
Definition: codegen_neuron_cpp_visitor.cpp:2010
+
nmodl::codegen::CodegenNeuronCppVisitor::print_net_move_call
void print_net_move_call(const ast::FunctionCall &node) override
Print call to net_move.
Definition: codegen_neuron_cpp_visitor.cpp:2114
nmodl::codegen::CodegenNeuronCppVisitor::thread_variable_name
std::string thread_variable_name(const ThreadVariableInfo &var_info, bool use_instance=true) const
Determine the C++ string to print for thread variables.
Definition: codegen_neuron_cpp_visitor.cpp:629
nmodl::codegen::naming::NODE_AREA_VARIABLE
static constexpr char NODE_AREA_VARIABLE[]
inbuilt neuron variable for area of the compartment
Definition: codegen_naming.hpp:57
-
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_state
void print_nrn_state() override
Print nrn_state / state update function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1671
+
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_state
void print_nrn_state() override
Print nrn_state / state update function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1675
nmodl::ast::Ast::is_function_block
virtual bool is_function_block() const noexcept
Check if the ast node is an instance of ast::FunctionBlock.
Definition: ast.cpp:142
nmodl::codegen::naming::NRN_ALLOC_METHOD
static constexpr char NRN_ALLOC_METHOD[]
nrn_alloc method in generated code
Definition: codegen_naming.hpp:150
-
nmodl::codegen::CodegenNeuronCppVisitor::print_initial_block
void print_initial_block(const ast::InitialBlock *node)
Print the initial block.
Definition: codegen_neuron_cpp_visitor.cpp:1455
+
nmodl::codegen::CodegenNeuronCppVisitor::print_initial_block
void print_initial_block(const ast::InitialBlock *node)
Print the initial block.
Definition: codegen_neuron_cpp_visitor.cpp:1450
nmodl::codegen::IndexVariableInfo::is_integer
bool is_integer
if this is an integer (e.g.
Definition: codegen_cpp_visitor.hpp:141
-
nmodl::codegen::CodegenNeuronCppVisitor::print_global_function_common_code
void print_global_function_common_code(BlockType type, const std::string &function_name="") override
Print common code for global functions like nrn_init, nrn_cur and nrn_state.
Definition: codegen_neuron_cpp_visitor.cpp:1477
+
nmodl::codegen::CodegenNeuronCppVisitor::print_global_function_common_code
void print_global_function_common_code(BlockType type, const std::string &function_name="") override
Print common code for global functions like nrn_init, nrn_cur and nrn_state.
Definition: codegen_neuron_cpp_visitor.cpp:1472
nmodl::codegen::CodegenNeuronCppVisitor::float_variable_name
std::string float_variable_name(const SymbolType &symbol, bool use_instance) const override
Determine the name of a float variable given its symbol.
Definition: codegen_neuron_cpp_visitor.cpp:581
nmodl::codegen::CodegenNeuronCppVisitor::print_function
void print_function(const ast::FunctionBlock &node) override
Print NMODL function in target backend code.
Definition: codegen_neuron_cpp_visitor.cpp:317
nmodl::ast::BreakpointBlock::get_statement_block
std::shared_ptr< StatementBlock > get_statement_block() const noexcept override
Getter for member variable BreakpointBlock::statement_block.
Definition: breakpoint_block.hpp:188
-
nmodl::codegen::CodegenNeuronCppVisitor::print_v_unused
void print_v_unused() const override
Set v_unused (voltage) for NRN_PRCELLSTATE feature.
Definition: codegen_neuron_cpp_visitor.cpp:2019
- +
nmodl::codegen::CodegenNeuronCppVisitor::print_v_unused
void print_v_unused() const override
Set v_unused (voltage) for NRN_PRCELLSTATE feature.
Definition: codegen_neuron_cpp_visitor.cpp:2025
+
nmodl::codegen::naming::CONDUCTANCE_VARIABLE
static constexpr char CONDUCTANCE_VARIABLE[]
range variable for conductance
Definition: codegen_naming.hpp:69
nmodl::codegen::CodegenNeuronCppVisitor::functor_params
ParamVector functor_params() override
The parameters of the Newton solver "functor".
Definition: codegen_neuron_cpp_visitor.cpp:819
codegen_cpp_visitor.hpp
Visitor for printing C++ code compatible with legacy api of CoreNEURON
@@ -2372,68 +2378,69 @@
nmodl::codegen::BlockType::Equation
@ Equation
breakpoint block
nmodl::codegen::naming::USE_TABLE_VARIABLE
static constexpr char USE_TABLE_VARIABLE[]
global variable to indicate if table is used
Definition: codegen_naming.hpp:72
nmodl::ast::WatchStatement
Represent WATCH statement in NMODL.
Definition: watch_statement.hpp:39
-
nmodl::codegen::CodegenNeuronCppVisitor::print_neuron_global_variable_declarations
void print_neuron_global_variable_declarations()
Print extern declarations for neuron global variables.
Definition: codegen_neuron_cpp_visitor.cpp:1292
+
nmodl::codegen::CodegenNeuronCppVisitor::print_neuron_global_variable_declarations
void print_neuron_global_variable_declarations()
Print extern declarations for neuron global variables.
Definition: codegen_neuron_cpp_visitor.cpp:1287
nmodl::ast::BreakpointBlock
Represents a BREAKPOINT block in NMODL.
Definition: breakpoint_block.hpp:53
-
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_cur_conductance_kernel
void print_nrn_cur_conductance_kernel(const ast::BreakpointBlock &node) override
Print the nrn_cur kernel with NMODL conductance keyword provisions.
Definition: codegen_neuron_cpp_visitor.cpp:1768
+
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_cur_conductance_kernel
void print_nrn_cur_conductance_kernel(const ast::BreakpointBlock &node) override
Print the nrn_cur kernel with NMODL conductance keyword provisions.
Definition: codegen_neuron_cpp_visitor.cpp:1772
nmodl::codegen::CodegenNeuronCppVisitor::int_variable_name
std::string int_variable_name(const IndexVariableInfo &symbol, const std::string &name, bool use_instance) const override
Determine the name of an int variable given its symbol.
Definition: codegen_neuron_cpp_visitor.cpp:601
nmodl::codegen::InterpreterWrapper
InterpreterWrapper
Enum to switch between HOC and Python wrappers for functions and procedures defined in mechanisms.
Definition: codegen_neuron_cpp_visitor.hpp:50
-
nmodl::codegen::CodegenNeuronCppVisitor::print_namespace_begin
void print_namespace_begin() override
Print start of namespaces.
Definition: codegen_neuron_cpp_visitor.cpp:1999
+
nmodl::codegen::CodegenNeuronCppVisitor::print_namespace_begin
void print_namespace_begin() override
Print start of namespaces.
Definition: codegen_neuron_cpp_visitor.cpp:2005
nmodl::codegen::CodegenNeuronCppVisitor::print_global_variables_for_hoc
void print_global_variables_for_hoc() override
Print byte arrays that register scalar and vector variables for hoc interface.
Definition: codegen_neuron_cpp_visitor.cpp:981
nmodl::codegen::CodegenNeuronCppVisitor::print_standard_includes
void print_standard_includes() override
Print standard C/C++ includes.
Definition: codegen_neuron_cpp_visitor.cpp:751
-
nmodl::codegen::CodegenNeuronCppVisitor::print_mechanism_range_var_structure
void print_mechanism_range_var_structure(bool print_initializers) override
Print the structure that wraps all range and int variables required for the NMODL.
Definition: codegen_neuron_cpp_visitor.cpp:1299
+
nmodl::codegen::CodegenNeuronCppVisitor::print_mechanism_range_var_structure
void print_mechanism_range_var_structure(bool print_initializers) override
Print the structure that wraps all range and int variables required for the NMODL.
Definition: codegen_neuron_cpp_visitor.cpp:1294
nmodl::codegen::CodegenNeuronCppVisitor::print_procedure
void print_procedure(const ast::ProcedureBlock &node) override
Print NMODL procedure in target backend code.
Definition: codegen_neuron_cpp_visitor.cpp:312
nmodl::codegen::CodegenNeuronCppVisitor::add_variable_tqitem
void add_variable_tqitem(std::vector< IndexVariableInfo > &variables) override
Add the variable tqitem during get_int_variables.
Definition: codegen_neuron_cpp_visitor.cpp:454
nmodl::codegen::CodegenNeuronCppVisitor::hoc_function_signature
std::string hoc_function_signature(const std::string &function_or_procedure_name) const
Get the signature of the hoc <func_or_proc_name> function.
Definition: codegen_neuron_cpp_visitor.cpp:532
nmodl::codegen::CodegenNeuronCppVisitor::print_namespace_start
void print_namespace_start() override
Prints the start of the neuron namespace.
Definition: codegen_neuron_cpp_visitor.cpp:558
-
nmodl::codegen::CodegenNeuronCppVisitor::print_thread_variables_structure
void print_thread_variables_structure(bool print_initializers)
Print the data structure used to access thread variables.
Definition: codegen_neuron_cpp_visitor.cpp:1423
+
nmodl::codegen::CodegenNeuronCppVisitor::print_thread_variables_structure
void print_thread_variables_structure(bool print_initializers)
Print the data structure used to access thread variables.
Definition: codegen_neuron_cpp_visitor.cpp:1418
nmodl::symtab::syminfo::to_string
std::string to_string(const T &obj)
Definition: symbol_properties.hpp:279
-
nmodl::codegen::CodegenNeuronCppVisitor::print_compute_functions
void print_compute_functions() override
Print all compute functions for every backend.
Definition: codegen_neuron_cpp_visitor.cpp:2041
+
nmodl::codegen::CodegenNeuronCppVisitor::print_compute_functions
void print_compute_functions() override
Print all compute functions for every backend.
Definition: codegen_neuron_cpp_visitor.cpp:2047
nmodl::codegen::naming::NRN_INIT_METHOD
static constexpr char NRN_INIT_METHOD[]
nrn_init method in generated code
Definition: codegen_naming.hpp:135
nmodl::ast::FunctionCall::get_arguments
const ExpressionVector & get_arguments() const noexcept
Getter for member variable FunctionCall::arguments.
Definition: function_call.hpp:166
-
nmodl::codegen::CodegenNeuronCppVisitor::print_thread_memory_callbacks
void print_thread_memory_callbacks()
Print thread variable (de-)initialization functions.
Definition: codegen_neuron_cpp_visitor.cpp:1258
+
nmodl::codegen::CodegenNeuronCppVisitor::print_thread_memory_callbacks
void print_thread_memory_callbacks()
Print thread variable (de-)initialization functions.
Definition: codegen_neuron_cpp_visitor.cpp:1253
nmodl::codegen::rename_net_receive_arguments
static void rename_net_receive_arguments(const ast::NetReceiveBlock &net_receive_node, const ast::Node &node)
Rename arguments to NET_RECEIVE block with corresponding pointer variable.
Definition: codegen_coreneuron_cpp_visitor.cpp:2363
-
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_cur_kernel
void print_nrn_cur_kernel(const ast::BreakpointBlock &node) override
Print main body of nrn_cur function.
Definition: codegen_neuron_cpp_visitor.cpp:1842
+
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_cur_kernel
void print_nrn_cur_kernel(const ast::BreakpointBlock &node) override
Print main body of nrn_cur function.
Definition: codegen_neuron_cpp_visitor.cpp:1846
nmodl::visitor::RenameVisitor
Blindly rename given variable to new name
Definition: rename_visitor.hpp:43
nmodl::codegen::naming::NRN_CUR_METHOD
static constexpr char NRN_CUR_METHOD[]
nrn_cur method in generated code
Definition: codegen_naming.hpp:156
nmodl::codegen::CodegenNeuronCppVisitor::conc_write_statement
std::string conc_write_statement(const std::string &ion_name, const std::string &concentration, int index) override
Generate Function call statement for nrn_wrote_conc.
Definition: codegen_neuron_cpp_visitor.cpp:569
nmodl::codegen::CodegenNeuronCppVisitor::print_mechanism_register
void print_mechanism_register() override
Print the mechanism registration function.
Definition: codegen_neuron_cpp_visitor.cpp:1101
codegen_utils.hpp
Implement utility functions for codegen visitors.
nmodl::codegen::naming::TQITEM_VARIABLE
static constexpr char TQITEM_VARIABLE[]
inbuilt neuron variable for tqitem process
Definition: codegen_naming.hpp:66
-
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_jacob
void print_nrn_jacob()
Print nrn_jacob function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1520
+
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_jacob
void print_nrn_jacob()
Print nrn_jacob function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1515
-
nmodl::codegen::CodegenNeuronCppVisitor::print_fast_imem_calculation
void print_fast_imem_calculation() override
Print fast membrane current calculation code.
Definition: codegen_neuron_cpp_visitor.cpp:1875
-
nmodl::codegen::CodegenNeuronCppVisitor::print_data_structures
void print_data_structures(bool print_initializers) override
Print all classes.
Definition: codegen_neuron_cpp_visitor.cpp:2009
+
nmodl::codegen::CodegenNeuronCppVisitor::print_fast_imem_calculation
void print_fast_imem_calculation() override
Print fast membrane current calculation code.
Definition: codegen_neuron_cpp_visitor.cpp:1879
+
nmodl::codegen::CodegenNeuronCppVisitor::print_data_structures
void print_data_structures(bool print_initializers) override
Print all classes.
Definition: codegen_neuron_cpp_visitor.cpp:2015
nmodl::ast::FunctionBlock::get_node_name
std::string get_node_name() const override
Return name of the node.
Definition: ast.cpp:3963
nmodl::codegen::CodegenNeuronCppVisitor::print_sdlists_init
void print_sdlists_init(bool print_initializers) override
Definition: codegen_neuron_cpp_visitor.cpp:778
nmodl::codegen::CodegenNeuronCppVisitor::external_method_arguments
const std::string external_method_arguments() noexcept override
Arguments for external functions called from generated code.
Definition: codegen_neuron_cpp_visitor.cpp:490
nmodl::codegen::CodegenNeuronCppVisitor::py_function_name
std::string py_function_name(const std::string &function_or_procedure_name) const
In non POINT_PROCESS mechanisms all functions and procedures need a py <func_or_proc_name> to be avai...
Definition: codegen_neuron_cpp_visitor.cpp:541
nmodl::codegen::ThreadVariableInfo::offset
size_t offset
The global variables ahead of this one require offset doubles to store.
Definition: codegen_neuron_cpp_visitor.hpp:71
-
nmodl::codegen::CodegenNeuronCppVisitor::print_node_data_structure
void print_node_data_structure(bool print_initializers)
Print the structure that wraps all node variables required for the NMODL.
Definition: codegen_neuron_cpp_visitor.cpp:1390
+
nmodl::codegen::CodegenNeuronCppVisitor::print_node_data_structure
void print_node_data_structure(bool print_initializers)
Print the structure that wraps all node variables required for the NMODL.
Definition: codegen_neuron_cpp_visitor.cpp:1385
nmodl::codegen::CppObjectSpecifier::Inline
@ Inline
nmodl::codegen::naming::INST_GLOBAL_MEMBER
static constexpr char INST_GLOBAL_MEMBER[]
instance struct member pointing to the global variable structure
Definition: codegen_naming.hpp:93
-
nmodl::codegen::CodegenNeuronCppVisitor::print_make_instance
void print_make_instance() const
Print make_*_instance.
Definition: codegen_neuron_cpp_visitor.cpp:1339
+
nmodl::codegen::CodegenNeuronCppVisitor::print_make_instance
void print_make_instance() const
Print make_*_instance.
Definition: codegen_neuron_cpp_visitor.cpp:1334
nmodl::codegen::CodegenNeuronCppVisitor::print_atomic_reduction_pragma
void print_atomic_reduction_pragma() override
Print atomic update pragma for reduction statements.
Definition: codegen_neuron_cpp_visitor.cpp:96
nmodl::symtab::syminfo::NmodlType
NmodlType
NMODL variable properties.
Definition: symbol_properties.hpp:116
nmodl::codegen::CodegenNeuronCppVisitor::print_namespace_stop
void print_namespace_stop() override
Prints the end of the neuron namespace.
Definition: codegen_neuron_cpp_visitor.cpp:564
nmodl::codegen::CodegenNeuronCppVisitor::print_setdata_functions
void print_setdata_functions()
Print NEURON functions related to setting global variables of the mechanism.
Definition: codegen_neuron_cpp_visitor.cpp:203
nmodl::codegen::ShadowUseStatement
Represents ion write statement during code generation.
Definition: codegen_cpp_visitor.hpp:166
-
nmodl::codegen::CodegenNeuronCppVisitor::print_mechanism_variables_macros
void print_mechanism_variables_macros()
Print mechanism variables' related macros.
Definition: codegen_neuron_cpp_visitor.cpp:1960
-
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_constructor
void print_nrn_constructor() override
Print nrn_constructor function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1554
+
nmodl::codegen::CodegenNeuronCppVisitor::print_mechanism_variables_macros
void print_mechanism_variables_macros()
Print mechanism variables' related macros.
Definition: codegen_neuron_cpp_visitor.cpp:1966
+
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_constructor
void print_nrn_constructor() override
Print nrn_constructor function definition.
Definition: codegen_neuron_cpp_visitor.cpp:1549
nmodl::codegen::CodegenNeuronCppVisitor::print_check_table_function_prototypes
void print_check_table_function_prototypes()
Print all check_* function declarations.
Definition: codegen_neuron_cpp_visitor.cpp:158
nmodl::ast::FunctionBlock::get_statement_block
std::shared_ptr< StatementBlock > get_statement_block() const noexcept override
Getter for member variable FunctionBlock::statement_block.
Definition: function_block.hpp:219
nmodl::codegen::BlockType
BlockType
Helper to represent various block types.
Definition: codegen_cpp_visitor.hpp:56
-
nmodl::codegen::CodegenNeuronCppVisitor::print_headers_include
void print_headers_include() override
Print all includes.
Definition: codegen_neuron_cpp_visitor.cpp:1927
+
nmodl::codegen::CodegenNeuronCppVisitor::print_headers_include
void print_headers_include() override
Print all includes.
Definition: codegen_neuron_cpp_visitor.cpp:1931
nmodl::codegen::CodegenNeuronCppVisitor::external_method_parameters
const ParamVector external_method_parameters(bool table=false) noexcept override
Parameters for functions in generated code that are called back from external code.
Definition: codegen_neuron_cpp_visitor.cpp:496
nmodl::codegen::CodegenNeuronCppVisitor::print_function_or_procedure
void print_function_or_procedure(const ast::Block &node, const std::string &name, const std::unordered_set< CppObjectSpecifier > &specifiers={ CppObjectSpecifier::Inline}) override
Print nmodl function or procedure (common code)
Definition: codegen_neuron_cpp_visitor.cpp:264
nmodl::codegen::naming::NRN_STATE_METHOD
static constexpr char NRN_STATE_METHOD[]
nrn_state method in generated code
Definition: codegen_naming.hpp:153
nmodl::codegen::ThreadVariableInfo::symbol
const std::shared_ptr< symtab::Symbol > symbol
Definition: codegen_neuron_cpp_visitor.hpp:61
config.h
Version information and units file path.
-
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_current
void print_nrn_current(const ast::BreakpointBlock &node) override
Print the nrn_current kernel.
Definition: codegen_neuron_cpp_visitor.cpp:1749
+
nmodl::codegen::CodegenNeuronCppVisitor::print_nrn_current
void print_nrn_current(const ast::BreakpointBlock &node) override
Print the nrn_current kernel.
Definition: codegen_neuron_cpp_visitor.cpp:1753
nmodl::codegen::CodegenNeuronCppVisitor::position_of_float_var
int position_of_float_var(const std::string &name) const override
Determine the position in the data array for a given float variable.
Definition: codegen_neuron_cpp_visitor.cpp:64
nmodl::codegen::CodegenNeuronCppVisitor::get_variable_name
std::string get_variable_name(const std::string &name, bool use_instance=true) const override
Determine variable name in the structure of mechanism properties.
Definition: codegen_neuron_cpp_visitor.cpp:660
-
nmodl::codegen::CodegenNeuronCppVisitor::print_make_node_data
void print_make_node_data() const
Print make_*_node_data.
Definition: codegen_neuron_cpp_visitor.cpp:1404
+
nmodl::codegen::naming::AREA_VARIABLE
static constexpr char AREA_VARIABLE[]
similar to node_area but user can explicitly declare it as area
Definition: codegen_naming.hpp:60
+
nmodl::codegen::CodegenNeuronCppVisitor::print_make_node_data
void print_make_node_data() const
Print make_*_node_data.
Definition: codegen_neuron_cpp_visitor.cpp:1399
nmodl::ast::Ast::get_statement_block
virtual std::shared_ptr< StatementBlock > get_statement_block() const
Return associated statement block for the AST node.
Definition: ast.cpp:32
nmodl::codegen::CodegenNeuronCppVisitor::simulator_name
std::string simulator_name() override
Name of the simulator the code was generated for.
Definition: codegen_neuron_cpp_visitor.cpp:44
nmodl::codegen::CodegenNeuronCppVisitor::print_function_procedure_helper
void print_function_procedure_helper(const ast::Block &node) override
Common helper function to help printing function or procedure blocks.
Definition: codegen_neuron_cpp_visitor.cpp:297
@@ -2442,21 +2449,22 @@
nmodl::codegen::CodegenNeuronCppVisitor::add_variable_point_process
void add_variable_point_process(std::vector< IndexVariableInfo > &variables) override
Add the variable point_process during get_int_variables.
Definition: codegen_neuron_cpp_visitor.cpp:462
rename_visitor.hpp
Blindly rename given variable to new name
nmodl::codegen::BlockType::State
@ State
derivative block
+
nmodl::codegen::naming::DIAM_VARIABLE
static constexpr char DIAM_VARIABLE[]
inbuilt neuron variable for diameter of the compartment
Definition: codegen_naming.hpp:54
nmodl::ast::Block::get_parameters
virtual const ArgumentVector & get_parameters() const
Definition: block.hpp:50
nmodl::visitor::VarUsageVisitor::variable_used
bool variable_used(const ast::Node &node, std::string name)
Definition: var_usage_visitor.cpp:26
nmodl::codegen::CodegenNeuronCppVisitor::nrn_thread_arguments
std::string nrn_thread_arguments() const override
Arguments for "_threadargs_" macro in neuron implementation.
Definition: codegen_neuron_cpp_visitor.cpp:503
nmodl::codegen::naming::CONDUCTANCE_UNUSED_VARIABLE
static constexpr char CONDUCTANCE_UNUSED_VARIABLE[]
range variable when conductance is not used (for vectorized model)
Definition: codegen_naming.hpp:75
-
nmodl::codegen::CodegenNeuronCppVisitor::print_codegen_routines
void print_codegen_routines() override
Print entry point to code generation.
Definition: codegen_neuron_cpp_visitor.cpp:2058
+
nmodl::codegen::CodegenNeuronCppVisitor::print_codegen_routines
void print_codegen_routines() override
Print entry point to code generation.
Definition: codegen_neuron_cpp_visitor.cpp:2064
nmodl::codegen::BlockType::Initial
@ Initial
initial block
nmodl::codegen::naming::NRN_POINTERINDEX
static constexpr char NRN_POINTERINDEX[]
hoc_nrnpointerindex name
Definition: codegen_naming.hpp:174
nmodl::codegen::CodegenNeuronCppVisitor::internal_method_parameters
ParamVector internal_method_parameters() override
Parameters for internally defined functions.
Definition: codegen_neuron_cpp_visitor.cpp:474
nmodl::ast::Ast::get_node_name
virtual std::string get_node_name() const
Return name of of the node.
Definition: ast.cpp:28
all.hpp
Auto generated AST classes declaration.
-
nmodl::codegen::CodegenNeuronCppVisitor::print_net_receive
void print_net_receive()
Print net_receive call-back.
Definition: codegen_neuron_cpp_visitor.cpp:2156
+
nmodl::codegen::CodegenNeuronCppVisitor::print_net_receive
void print_net_receive()
Print net_receive call-back.
Definition: codegen_neuron_cpp_visitor.cpp:2162
nmodl::codegen::CodegenNeuronCppVisitor::print_function_prototypes
void print_function_prototypes() override
Print function and procedures prototype declaration.
Definition: codegen_neuron_cpp_visitor.cpp:253
nmodl::codegen::CodegenNeuronCppVisitor::print_mechanism_global_var_structure
void print_mechanism_global_var_structure(bool print_initializers) override
Print the structure that wraps all global variables used in the NMODL.
Definition: codegen_neuron_cpp_visitor.cpp:827
-
nmodl::codegen::CodegenNeuronCppVisitor::print_global_macros
void print_global_macros()
Print NEURON global variable macros.
Definition: codegen_neuron_cpp_visitor.cpp:1943
+
nmodl::codegen::CodegenNeuronCppVisitor::print_global_macros
void print_global_macros()
Print NEURON global variable macros.
Definition: codegen_neuron_cpp_visitor.cpp:1949
nmodl::codegen::CodegenCppVisitor::ParamVector
std::vector< std::tuple< std::string, std::string, std::string, std::string > > ParamVector
A vector of parameters represented by a 4-tuple of strings:
Definition: codegen_cpp_visitor.hpp:266
nmodl::codegen::naming::ION_VARNAME_PREFIX
static constexpr char ION_VARNAME_PREFIX[]
prefix for ion variable
Definition: codegen_naming.hpp:171
diff --git a/notebooks/nmodl-kinetic-schemes.ipynb b/notebooks/nmodl-kinetic-schemes.ipynb index a3b84c640..9423ac0c3 100644 --- a/notebooks/nmodl-kinetic-schemes.ipynb +++ b/notebooks/nmodl-kinetic-schemes.ipynb @@ -152,10 +152,10 @@ "execution_count": 1, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:09.233551Z", - "iopub.status.busy": "2024-07-05T14:21:09.233360Z", - "iopub.status.idle": "2024-07-05T14:21:09.971964Z", - "shell.execute_reply": "2024-07-05T14:21:09.971253Z" + "iopub.execute_input": "2024-07-08T14:19:11.343181Z", + "iopub.status.busy": "2024-07-08T14:19:11.342948Z", + "iopub.status.idle": "2024-07-08T14:19:12.142002Z", + "shell.execute_reply": "2024-07-08T14:19:12.141214Z" } }, "outputs": [], @@ -169,10 +169,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:09.975041Z", - "iopub.status.busy": "2024-07-05T14:21:09.974634Z", - "iopub.status.idle": "2024-07-05T14:21:10.001923Z", - "shell.execute_reply": "2024-07-05T14:21:10.001287Z" + "iopub.execute_input": "2024-07-08T14:19:12.145153Z", + "iopub.status.busy": "2024-07-08T14:19:12.144926Z", + "iopub.status.idle": "2024-07-08T14:19:12.173471Z", + "shell.execute_reply": "2024-07-08T14:19:12.172816Z" } }, "outputs": [], @@ -277,10 +277,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:10.005002Z", - "iopub.status.busy": "2024-07-05T14:21:10.004689Z", - "iopub.status.idle": "2024-07-05T14:21:10.009712Z", - "shell.execute_reply": "2024-07-05T14:21:10.009056Z" + "iopub.execute_input": "2024-07-08T14:19:12.176565Z", + "iopub.status.busy": "2024-07-08T14:19:12.176282Z", + "iopub.status.idle": "2024-07-08T14:19:12.181063Z", + "shell.execute_reply": "2024-07-08T14:19:12.180392Z" } }, "outputs": [ @@ -323,10 +323,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:10.038573Z", - "iopub.status.busy": "2024-07-05T14:21:10.038045Z", - "iopub.status.idle": "2024-07-05T14:21:10.041944Z", - "shell.execute_reply": "2024-07-05T14:21:10.041310Z" + "iopub.execute_input": "2024-07-08T14:19:12.212484Z", + "iopub.status.busy": "2024-07-08T14:19:12.212210Z", + "iopub.status.idle": "2024-07-08T14:19:12.217225Z", + "shell.execute_reply": "2024-07-08T14:19:12.216517Z" } }, "outputs": [ @@ -367,10 +367,10 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:10.044424Z", - "iopub.status.busy": "2024-07-05T14:21:10.044080Z", - "iopub.status.idle": "2024-07-05T14:21:10.047715Z", - "shell.execute_reply": "2024-07-05T14:21:10.047069Z" + "iopub.execute_input": "2024-07-08T14:19:12.219699Z", + "iopub.status.busy": "2024-07-08T14:19:12.219477Z", + "iopub.status.idle": "2024-07-08T14:19:12.223731Z", + "shell.execute_reply": "2024-07-08T14:19:12.223002Z" }, "scrolled": true }, @@ -412,10 +412,10 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:10.050110Z", - "iopub.status.busy": "2024-07-05T14:21:10.049673Z", - "iopub.status.idle": "2024-07-05T14:21:10.053448Z", - "shell.execute_reply": "2024-07-05T14:21:10.052823Z" + "iopub.execute_input": "2024-07-08T14:19:12.226274Z", + "iopub.status.busy": "2024-07-08T14:19:12.226063Z", + "iopub.status.idle": "2024-07-08T14:19:12.230139Z", + "shell.execute_reply": "2024-07-08T14:19:12.229453Z" }, "scrolled": true }, @@ -459,10 +459,10 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:10.055917Z", - "iopub.status.busy": "2024-07-05T14:21:10.055579Z", - "iopub.status.idle": "2024-07-05T14:21:10.059677Z", - "shell.execute_reply": "2024-07-05T14:21:10.059013Z" + "iopub.execute_input": "2024-07-08T14:19:12.233438Z", + "iopub.status.busy": "2024-07-08T14:19:12.232862Z", + "iopub.status.idle": "2024-07-08T14:19:12.238022Z", + "shell.execute_reply": "2024-07-08T14:19:12.237325Z" } }, "outputs": [ diff --git a/notebooks/nmodl-python-tutorial.ipynb b/notebooks/nmodl-python-tutorial.ipynb index 41d803bba..6bbe2e92e 100644 --- a/notebooks/nmodl-python-tutorial.ipynb +++ b/notebooks/nmodl-python-tutorial.ipynb @@ -30,10 +30,10 @@ "execution_count": 1, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:14.945002Z", - "iopub.status.busy": "2024-07-05T14:21:14.944804Z", - "iopub.status.idle": "2024-07-05T14:21:15.691254Z", - "shell.execute_reply": "2024-07-05T14:21:15.690532Z" + "iopub.execute_input": "2024-07-08T14:19:17.773745Z", + "iopub.status.busy": "2024-07-08T14:19:17.773508Z", + "iopub.status.idle": "2024-07-08T14:19:18.583317Z", + "shell.execute_reply": "2024-07-08T14:19:18.582499Z" } }, "outputs": [], @@ -63,10 +63,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.694514Z", - "iopub.status.busy": "2024-07-05T14:21:15.694056Z", - "iopub.status.idle": "2024-07-05T14:21:15.718735Z", - "shell.execute_reply": "2024-07-05T14:21:15.718124Z" + "iopub.execute_input": "2024-07-08T14:19:18.586574Z", + "iopub.status.busy": "2024-07-08T14:19:18.586304Z", + "iopub.status.idle": "2024-07-08T14:19:18.613678Z", + "shell.execute_reply": "2024-07-08T14:19:18.612926Z" } }, "outputs": [], @@ -86,10 +86,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.721535Z", - "iopub.status.busy": "2024-07-05T14:21:15.721147Z", - "iopub.status.idle": "2024-07-05T14:21:15.724718Z", - "shell.execute_reply": "2024-07-05T14:21:15.724167Z" + "iopub.execute_input": "2024-07-08T14:19:18.616835Z", + "iopub.status.busy": "2024-07-08T14:19:18.616603Z", + "iopub.status.idle": "2024-07-08T14:19:18.620503Z", + "shell.execute_reply": "2024-07-08T14:19:18.619909Z" } }, "outputs": [], @@ -152,10 +152,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.727245Z", - "iopub.status.busy": "2024-07-05T14:21:15.726869Z", - "iopub.status.idle": "2024-07-05T14:21:15.731580Z", - "shell.execute_reply": "2024-07-05T14:21:15.730940Z" + "iopub.execute_input": "2024-07-08T14:19:18.623065Z", + "iopub.status.busy": "2024-07-08T14:19:18.622848Z", + "iopub.status.idle": "2024-07-08T14:19:18.627437Z", + "shell.execute_reply": "2024-07-08T14:19:18.626783Z" } }, "outputs": [], @@ -183,10 +183,10 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.733982Z", - "iopub.status.busy": "2024-07-05T14:21:15.733638Z", - "iopub.status.idle": "2024-07-05T14:21:15.737180Z", - "shell.execute_reply": "2024-07-05T14:21:15.736567Z" + "iopub.execute_input": "2024-07-08T14:19:18.630025Z", + "iopub.status.busy": "2024-07-08T14:19:18.629756Z", + "iopub.status.idle": "2024-07-08T14:19:18.633773Z", + "shell.execute_reply": "2024-07-08T14:19:18.633051Z" } }, "outputs": [ @@ -235,10 +235,10 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.739589Z", - "iopub.status.busy": "2024-07-05T14:21:15.739255Z", - "iopub.status.idle": "2024-07-05T14:21:15.743109Z", - "shell.execute_reply": "2024-07-05T14:21:15.742499Z" + "iopub.execute_input": "2024-07-08T14:19:18.636311Z", + "iopub.status.busy": "2024-07-08T14:19:18.636114Z", + "iopub.status.idle": "2024-07-08T14:19:18.640682Z", + "shell.execute_reply": "2024-07-08T14:19:18.640124Z" } }, "outputs": [], @@ -260,10 +260,10 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.745584Z", - "iopub.status.busy": "2024-07-05T14:21:15.745100Z", - "iopub.status.idle": "2024-07-05T14:21:15.748776Z", - "shell.execute_reply": "2024-07-05T14:21:15.748153Z" + "iopub.execute_input": "2024-07-08T14:19:18.643170Z", + "iopub.status.busy": "2024-07-08T14:19:18.642970Z", + "iopub.status.idle": "2024-07-08T14:19:18.646781Z", + "shell.execute_reply": "2024-07-08T14:19:18.646083Z" } }, "outputs": [ @@ -297,10 +297,10 @@ "execution_count": 8, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.751231Z", - "iopub.status.busy": "2024-07-05T14:21:15.750748Z", - "iopub.status.idle": "2024-07-05T14:21:15.758064Z", - "shell.execute_reply": "2024-07-05T14:21:15.757435Z" + "iopub.execute_input": "2024-07-08T14:19:18.649463Z", + "iopub.status.busy": "2024-07-08T14:19:18.649062Z", + "iopub.status.idle": "2024-07-08T14:19:18.656877Z", + "shell.execute_reply": "2024-07-08T14:19:18.656192Z" } }, "outputs": [ @@ -365,10 +365,10 @@ "execution_count": 9, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.760443Z", - "iopub.status.busy": "2024-07-05T14:21:15.760107Z", - "iopub.status.idle": "2024-07-05T14:21:15.764246Z", - "shell.execute_reply": "2024-07-05T14:21:15.763621Z" + "iopub.execute_input": "2024-07-08T14:19:18.659462Z", + "iopub.status.busy": "2024-07-08T14:19:18.659251Z", + "iopub.status.idle": "2024-07-08T14:19:18.663832Z", + "shell.execute_reply": "2024-07-08T14:19:18.663176Z" } }, "outputs": [ @@ -416,10 +416,10 @@ "execution_count": 10, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.766684Z", - "iopub.status.busy": "2024-07-05T14:21:15.766443Z", - "iopub.status.idle": "2024-07-05T14:21:15.769766Z", - "shell.execute_reply": "2024-07-05T14:21:15.769138Z" + "iopub.execute_input": "2024-07-08T14:19:18.666269Z", + "iopub.status.busy": "2024-07-08T14:19:18.666074Z", + "iopub.status.idle": "2024-07-08T14:19:18.669857Z", + "shell.execute_reply": "2024-07-08T14:19:18.669188Z" } }, "outputs": [], @@ -441,10 +441,10 @@ "execution_count": 11, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.772077Z", - "iopub.status.busy": "2024-07-05T14:21:15.771878Z", - "iopub.status.idle": "2024-07-05T14:21:15.775486Z", - "shell.execute_reply": "2024-07-05T14:21:15.774822Z" + "iopub.execute_input": "2024-07-08T14:19:18.672469Z", + "iopub.status.busy": "2024-07-08T14:19:18.672262Z", + "iopub.status.idle": "2024-07-08T14:19:18.676241Z", + "shell.execute_reply": "2024-07-08T14:19:18.675532Z" } }, "outputs": [ @@ -510,10 +510,10 @@ "execution_count": 12, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.778089Z", - "iopub.status.busy": "2024-07-05T14:21:15.777704Z", - "iopub.status.idle": "2024-07-05T14:21:15.780991Z", - "shell.execute_reply": "2024-07-05T14:21:15.780332Z" + "iopub.execute_input": "2024-07-08T14:19:18.678863Z", + "iopub.status.busy": "2024-07-08T14:19:18.678417Z", + "iopub.status.idle": "2024-07-08T14:19:18.682345Z", + "shell.execute_reply": "2024-07-08T14:19:18.681608Z" } }, "outputs": [ @@ -548,10 +548,10 @@ "execution_count": 13, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.783522Z", - "iopub.status.busy": "2024-07-05T14:21:15.783156Z", - "iopub.status.idle": "2024-07-05T14:21:15.786554Z", - "shell.execute_reply": "2024-07-05T14:21:15.785874Z" + "iopub.execute_input": "2024-07-08T14:19:18.684840Z", + "iopub.status.busy": "2024-07-08T14:19:18.684633Z", + "iopub.status.idle": "2024-07-08T14:19:18.688452Z", + "shell.execute_reply": "2024-07-08T14:19:18.687745Z" } }, "outputs": [ @@ -584,10 +584,10 @@ "execution_count": 14, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.789101Z", - "iopub.status.busy": "2024-07-05T14:21:15.788742Z", - "iopub.status.idle": "2024-07-05T14:21:15.792205Z", - "shell.execute_reply": "2024-07-05T14:21:15.791559Z" + "iopub.execute_input": "2024-07-08T14:19:18.690987Z", + "iopub.status.busy": "2024-07-08T14:19:18.690790Z", + "iopub.status.idle": "2024-07-08T14:19:18.694530Z", + "shell.execute_reply": "2024-07-08T14:19:18.693795Z" } }, "outputs": [ @@ -622,10 +622,10 @@ "execution_count": 15, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.794735Z", - "iopub.status.busy": "2024-07-05T14:21:15.794357Z", - "iopub.status.idle": "2024-07-05T14:21:15.798261Z", - "shell.execute_reply": "2024-07-05T14:21:15.797605Z" + "iopub.execute_input": "2024-07-08T14:19:18.696897Z", + "iopub.status.busy": "2024-07-08T14:19:18.696703Z", + "iopub.status.idle": "2024-07-08T14:19:18.701003Z", + "shell.execute_reply": "2024-07-08T14:19:18.700285Z" } }, "outputs": [ @@ -669,10 +669,10 @@ "execution_count": 16, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.800806Z", - "iopub.status.busy": "2024-07-05T14:21:15.800446Z", - "iopub.status.idle": "2024-07-05T14:21:15.805642Z", - "shell.execute_reply": "2024-07-05T14:21:15.804987Z" + "iopub.execute_input": "2024-07-08T14:19:18.703593Z", + "iopub.status.busy": "2024-07-08T14:19:18.703371Z", + "iopub.status.idle": "2024-07-08T14:19:18.709089Z", + "shell.execute_reply": "2024-07-08T14:19:18.708371Z" } }, "outputs": [ @@ -733,10 +733,10 @@ "execution_count": 17, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.808183Z", - "iopub.status.busy": "2024-07-05T14:21:15.807809Z", - "iopub.status.idle": "2024-07-05T14:21:15.811249Z", - "shell.execute_reply": "2024-07-05T14:21:15.810663Z" + "iopub.execute_input": "2024-07-08T14:19:18.711847Z", + "iopub.status.busy": "2024-07-08T14:19:18.711608Z", + "iopub.status.idle": "2024-07-08T14:19:18.715630Z", + "shell.execute_reply": "2024-07-08T14:19:18.714908Z" } }, "outputs": [], @@ -761,10 +761,10 @@ "execution_count": 18, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.813704Z", - "iopub.status.busy": "2024-07-05T14:21:15.813344Z", - "iopub.status.idle": "2024-07-05T14:21:15.823586Z", - "shell.execute_reply": "2024-07-05T14:21:15.823016Z" + "iopub.execute_input": "2024-07-08T14:19:18.718205Z", + "iopub.status.busy": "2024-07-08T14:19:18.717990Z", + "iopub.status.idle": "2024-07-08T14:19:18.728725Z", + "shell.execute_reply": "2024-07-08T14:19:18.728117Z" } }, "outputs": [], @@ -857,10 +857,10 @@ "execution_count": 19, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.826009Z", - "iopub.status.busy": "2024-07-05T14:21:15.825647Z", - "iopub.status.idle": "2024-07-05T14:21:15.829100Z", - "shell.execute_reply": "2024-07-05T14:21:15.828448Z" + "iopub.execute_input": "2024-07-08T14:19:18.731260Z", + "iopub.status.busy": "2024-07-08T14:19:18.731026Z", + "iopub.status.idle": "2024-07-08T14:19:18.735329Z", + "shell.execute_reply": "2024-07-08T14:19:18.734631Z" } }, "outputs": [ @@ -897,10 +897,10 @@ "execution_count": 20, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:15.831705Z", - "iopub.status.busy": "2024-07-05T14:21:15.831344Z", - "iopub.status.idle": "2024-07-05T14:21:15.836721Z", - "shell.execute_reply": "2024-07-05T14:21:15.836059Z" + "iopub.execute_input": "2024-07-08T14:19:18.737758Z", + "iopub.status.busy": "2024-07-08T14:19:18.737554Z", + "iopub.status.idle": "2024-07-08T14:19:18.743435Z", + "shell.execute_reply": "2024-07-08T14:19:18.742749Z" } }, "outputs": [ diff --git a/notebooks/nmodl-sympy-conductance.ipynb b/notebooks/nmodl-sympy-conductance.ipynb index c67b5c06f..6e10fa6ad 100644 --- a/notebooks/nmodl-sympy-conductance.ipynb +++ b/notebooks/nmodl-sympy-conductance.ipynb @@ -86,10 +86,10 @@ "execution_count": 1, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:17.997610Z", - "iopub.status.busy": "2024-07-05T14:21:17.997078Z", - "iopub.status.idle": "2024-07-05T14:21:18.738526Z", - "shell.execute_reply": "2024-07-05T14:21:18.737746Z" + "iopub.execute_input": "2024-07-08T14:19:21.317356Z", + "iopub.status.busy": "2024-07-08T14:19:21.316786Z", + "iopub.status.idle": "2024-07-08T14:19:22.121495Z", + "shell.execute_reply": "2024-07-08T14:19:22.120676Z" } }, "outputs": [], @@ -103,10 +103,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:18.741634Z", - "iopub.status.busy": "2024-07-05T14:21:18.741215Z", - "iopub.status.idle": "2024-07-05T14:21:18.768427Z", - "shell.execute_reply": "2024-07-05T14:21:18.767699Z" + "iopub.execute_input": "2024-07-08T14:19:22.125074Z", + "iopub.status.busy": "2024-07-08T14:19:22.124482Z", + "iopub.status.idle": "2024-07-08T14:19:22.153146Z", + "shell.execute_reply": "2024-07-08T14:19:22.152468Z" } }, "outputs": [], @@ -149,10 +149,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:18.771220Z", - "iopub.status.busy": "2024-07-05T14:21:18.770972Z", - "iopub.status.idle": "2024-07-05T14:21:19.027232Z", - "shell.execute_reply": "2024-07-05T14:21:19.026555Z" + "iopub.execute_input": "2024-07-08T14:19:22.156578Z", + "iopub.status.busy": "2024-07-08T14:19:22.156052Z", + "iopub.status.idle": "2024-07-08T14:19:22.440666Z", + "shell.execute_reply": "2024-07-08T14:19:22.439889Z" } }, "outputs": [ @@ -196,10 +196,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:19.029882Z", - "iopub.status.busy": "2024-07-05T14:21:19.029540Z", - "iopub.status.idle": "2024-07-05T14:21:19.176209Z", - "shell.execute_reply": "2024-07-05T14:21:19.175391Z" + "iopub.execute_input": "2024-07-08T14:19:22.443723Z", + "iopub.status.busy": "2024-07-08T14:19:22.443084Z", + "iopub.status.idle": "2024-07-08T14:19:22.597116Z", + "shell.execute_reply": "2024-07-08T14:19:22.596399Z" } }, "outputs": [ @@ -243,10 +243,10 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:19.179397Z", - "iopub.status.busy": "2024-07-05T14:21:19.178856Z", - "iopub.status.idle": "2024-07-05T14:21:19.187019Z", - "shell.execute_reply": "2024-07-05T14:21:19.186366Z" + "iopub.execute_input": "2024-07-08T14:19:22.599924Z", + "iopub.status.busy": "2024-07-08T14:19:22.599697Z", + "iopub.status.idle": "2024-07-08T14:19:22.608506Z", + "shell.execute_reply": "2024-07-08T14:19:22.607749Z" } }, "outputs": [ @@ -290,10 +290,10 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:19.189557Z", - "iopub.status.busy": "2024-07-05T14:21:19.189065Z", - "iopub.status.idle": "2024-07-05T14:21:19.206236Z", - "shell.execute_reply": "2024-07-05T14:21:19.205688Z" + "iopub.execute_input": "2024-07-08T14:19:22.611253Z", + "iopub.status.busy": "2024-07-08T14:19:22.611025Z", + "iopub.status.idle": "2024-07-08T14:19:22.629729Z", + "shell.execute_reply": "2024-07-08T14:19:22.629073Z" } }, "outputs": [ @@ -337,10 +337,10 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:19.208598Z", - "iopub.status.busy": "2024-07-05T14:21:19.208304Z", - "iopub.status.idle": "2024-07-05T14:21:19.331870Z", - "shell.execute_reply": "2024-07-05T14:21:19.331230Z" + "iopub.execute_input": "2024-07-08T14:19:22.632430Z", + "iopub.status.busy": "2024-07-08T14:19:22.632200Z", + "iopub.status.idle": "2024-07-08T14:19:22.762561Z", + "shell.execute_reply": "2024-07-08T14:19:22.761830Z" } }, "outputs": [ @@ -400,10 +400,10 @@ "execution_count": 8, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:19.334574Z", - "iopub.status.busy": "2024-07-05T14:21:19.334335Z", - "iopub.status.idle": "2024-07-05T14:21:19.433413Z", - "shell.execute_reply": "2024-07-05T14:21:19.432838Z" + "iopub.execute_input": "2024-07-08T14:19:22.765393Z", + "iopub.status.busy": "2024-07-08T14:19:22.765161Z", + "iopub.status.idle": "2024-07-08T14:19:22.870422Z", + "shell.execute_reply": "2024-07-08T14:19:22.869740Z" } }, "outputs": [ @@ -456,10 +456,10 @@ "execution_count": 9, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:19.435928Z", - "iopub.status.busy": "2024-07-05T14:21:19.435542Z", - "iopub.status.idle": "2024-07-05T14:21:19.506862Z", - "shell.execute_reply": "2024-07-05T14:21:19.506212Z" + "iopub.execute_input": "2024-07-08T14:19:22.873175Z", + "iopub.status.busy": "2024-07-08T14:19:22.872935Z", + "iopub.status.idle": "2024-07-08T14:19:22.948171Z", + "shell.execute_reply": "2024-07-08T14:19:22.947424Z" } }, "outputs": [ diff --git a/notebooks/nmodl-sympy-solver-cnexp.ipynb b/notebooks/nmodl-sympy-solver-cnexp.ipynb index 746260b4d..012809611 100644 --- a/notebooks/nmodl-sympy-solver-cnexp.ipynb +++ b/notebooks/nmodl-sympy-solver-cnexp.ipynb @@ -62,10 +62,10 @@ "execution_count": 1, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:21.082557Z", - "iopub.status.busy": "2024-07-05T14:21:21.081964Z", - "iopub.status.idle": "2024-07-05T14:21:21.826924Z", - "shell.execute_reply": "2024-07-05T14:21:21.826149Z" + "iopub.execute_input": "2024-07-08T14:19:24.812751Z", + "iopub.status.busy": "2024-07-08T14:19:24.812436Z", + "iopub.status.idle": "2024-07-08T14:19:25.623956Z", + "shell.execute_reply": "2024-07-08T14:19:25.623195Z" } }, "outputs": [], @@ -79,10 +79,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:21.830127Z", - "iopub.status.busy": "2024-07-05T14:21:21.829668Z", - "iopub.status.idle": "2024-07-05T14:21:21.857147Z", - "shell.execute_reply": "2024-07-05T14:21:21.856426Z" + "iopub.execute_input": "2024-07-08T14:19:25.627345Z", + "iopub.status.busy": "2024-07-08T14:19:25.627111Z", + "iopub.status.idle": "2024-07-08T14:19:25.658122Z", + "shell.execute_reply": "2024-07-08T14:19:25.657332Z" } }, "outputs": [], @@ -123,10 +123,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:21.859819Z", - "iopub.status.busy": "2024-07-05T14:21:21.859566Z", - "iopub.status.idle": "2024-07-05T14:21:22.307680Z", - "shell.execute_reply": "2024-07-05T14:21:22.306951Z" + "iopub.execute_input": "2024-07-08T14:19:25.661405Z", + "iopub.status.busy": "2024-07-08T14:19:25.661126Z", + "iopub.status.idle": "2024-07-08T14:19:26.125710Z", + "shell.execute_reply": "2024-07-08T14:19:26.124931Z" } }, "outputs": [ @@ -165,10 +165,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:22.310411Z", - "iopub.status.busy": "2024-07-05T14:21:22.309967Z", - "iopub.status.idle": "2024-07-05T14:21:22.445669Z", - "shell.execute_reply": "2024-07-05T14:21:22.444989Z" + "iopub.execute_input": "2024-07-08T14:19:26.128804Z", + "iopub.status.busy": "2024-07-08T14:19:26.128316Z", + "iopub.status.idle": "2024-07-08T14:19:26.268524Z", + "shell.execute_reply": "2024-07-08T14:19:26.267745Z" } }, "outputs": [ @@ -207,10 +207,10 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:22.448469Z", - "iopub.status.busy": "2024-07-05T14:21:22.448076Z", - "iopub.status.idle": "2024-07-05T14:21:22.679259Z", - "shell.execute_reply": "2024-07-05T14:21:22.678593Z" + "iopub.execute_input": "2024-07-08T14:19:26.271283Z", + "iopub.status.busy": "2024-07-08T14:19:26.271054Z", + "iopub.status.idle": "2024-07-08T14:19:26.510893Z", + "shell.execute_reply": "2024-07-08T14:19:26.510102Z" } }, "outputs": [ @@ -255,10 +255,10 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:22.682003Z", - "iopub.status.busy": "2024-07-05T14:21:22.681602Z", - "iopub.status.idle": "2024-07-05T14:21:22.873830Z", - "shell.execute_reply": "2024-07-05T14:21:22.873103Z" + "iopub.execute_input": "2024-07-08T14:19:26.513860Z", + "iopub.status.busy": "2024-07-08T14:19:26.513445Z", + "iopub.status.idle": "2024-07-08T14:19:26.712459Z", + "shell.execute_reply": "2024-07-08T14:19:26.711798Z" } }, "outputs": [ @@ -297,10 +297,10 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:22.876732Z", - "iopub.status.busy": "2024-07-05T14:21:22.876316Z", - "iopub.status.idle": "2024-07-05T14:21:24.273155Z", - "shell.execute_reply": "2024-07-05T14:21:24.272465Z" + "iopub.execute_input": "2024-07-08T14:19:26.715318Z", + "iopub.status.busy": "2024-07-08T14:19:26.714907Z", + "iopub.status.idle": "2024-07-08T14:19:28.190861Z", + "shell.execute_reply": "2024-07-08T14:19:28.190133Z" } }, "outputs": [ @@ -345,10 +345,10 @@ "execution_count": 8, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:24.276066Z", - "iopub.status.busy": "2024-07-05T14:21:24.275553Z", - "iopub.status.idle": "2024-07-05T14:21:26.074496Z", - "shell.execute_reply": "2024-07-05T14:21:26.073756Z" + "iopub.execute_input": "2024-07-08T14:19:28.193841Z", + "iopub.status.busy": "2024-07-08T14:19:28.193380Z", + "iopub.status.idle": "2024-07-08T14:19:30.056617Z", + "shell.execute_reply": "2024-07-08T14:19:30.055913Z" } }, "outputs": [ diff --git a/notebooks/nmodl-sympy-solver-derivimplicit.ipynb b/notebooks/nmodl-sympy-solver-derivimplicit.ipynb index 4c70d4e51..4a707599d 100644 --- a/notebooks/nmodl-sympy-solver-derivimplicit.ipynb +++ b/notebooks/nmodl-sympy-solver-derivimplicit.ipynb @@ -39,10 +39,10 @@ "execution_count": 1, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:27.681994Z", - "iopub.status.busy": "2024-07-05T14:21:27.681793Z", - "iopub.status.idle": "2024-07-05T14:21:28.433607Z", - "shell.execute_reply": "2024-07-05T14:21:28.432876Z" + "iopub.execute_input": "2024-07-08T14:19:32.049185Z", + "iopub.status.busy": "2024-07-08T14:19:32.048967Z", + "iopub.status.idle": "2024-07-08T14:19:32.852052Z", + "shell.execute_reply": "2024-07-08T14:19:32.851318Z" } }, "outputs": [], @@ -56,10 +56,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:28.436672Z", - "iopub.status.busy": "2024-07-05T14:21:28.436418Z", - "iopub.status.idle": "2024-07-05T14:21:28.463108Z", - "shell.execute_reply": "2024-07-05T14:21:28.462516Z" + "iopub.execute_input": "2024-07-08T14:19:32.855192Z", + "iopub.status.busy": "2024-07-08T14:19:32.854969Z", + "iopub.status.idle": "2024-07-08T14:19:32.884763Z", + "shell.execute_reply": "2024-07-08T14:19:32.883964Z" } }, "outputs": [], @@ -100,10 +100,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:28.465795Z", - "iopub.status.busy": "2024-07-05T14:21:28.465409Z", - "iopub.status.idle": "2024-07-05T14:21:28.939324Z", - "shell.execute_reply": "2024-07-05T14:21:28.938604Z" + "iopub.execute_input": "2024-07-08T14:19:32.888300Z", + "iopub.status.busy": "2024-07-08T14:19:32.887833Z", + "iopub.status.idle": "2024-07-08T14:19:33.384183Z", + "shell.execute_reply": "2024-07-08T14:19:33.383395Z" } }, "outputs": [ @@ -165,10 +165,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:28.941963Z", - "iopub.status.busy": "2024-07-05T14:21:28.941698Z", - "iopub.status.idle": "2024-07-05T14:21:29.157304Z", - "shell.execute_reply": "2024-07-05T14:21:29.156681Z" + "iopub.execute_input": "2024-07-08T14:19:33.387641Z", + "iopub.status.busy": "2024-07-08T14:19:33.387030Z", + "iopub.status.idle": "2024-07-08T14:19:33.615481Z", + "shell.execute_reply": "2024-07-08T14:19:33.614713Z" } }, "outputs": [ diff --git a/notebooks/nmodl-sympy-solver-sparse.ipynb b/notebooks/nmodl-sympy-solver-sparse.ipynb index de9653d18..558fe9452 100644 --- a/notebooks/nmodl-sympy-solver-sparse.ipynb +++ b/notebooks/nmodl-sympy-solver-sparse.ipynb @@ -39,10 +39,10 @@ "execution_count": 1, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:30.423828Z", - "iopub.status.busy": "2024-07-05T14:21:30.423267Z", - "iopub.status.idle": "2024-07-05T14:21:31.165732Z", - "shell.execute_reply": "2024-07-05T14:21:31.164876Z" + "iopub.execute_input": "2024-07-08T14:19:35.091365Z", + "iopub.status.busy": "2024-07-08T14:19:35.091139Z", + "iopub.status.idle": "2024-07-08T14:19:35.902205Z", + "shell.execute_reply": "2024-07-08T14:19:35.901295Z" } }, "outputs": [], @@ -56,10 +56,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:31.169076Z", - "iopub.status.busy": "2024-07-05T14:21:31.168671Z", - "iopub.status.idle": "2024-07-05T14:21:31.195296Z", - "shell.execute_reply": "2024-07-05T14:21:31.194695Z" + "iopub.execute_input": "2024-07-08T14:19:35.906761Z", + "iopub.status.busy": "2024-07-08T14:19:35.905989Z", + "iopub.status.idle": "2024-07-08T14:19:35.935381Z", + "shell.execute_reply": "2024-07-08T14:19:35.934578Z" } }, "outputs": [], @@ -100,10 +100,10 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:31.197866Z", - "iopub.status.busy": "2024-07-05T14:21:31.197551Z", - "iopub.status.idle": "2024-07-05T14:21:31.655770Z", - "shell.execute_reply": "2024-07-05T14:21:31.655040Z" + "iopub.execute_input": "2024-07-08T14:19:35.938636Z", + "iopub.status.busy": "2024-07-08T14:19:35.938316Z", + "iopub.status.idle": "2024-07-08T14:19:36.446881Z", + "shell.execute_reply": "2024-07-08T14:19:36.446144Z" } }, "outputs": [ @@ -165,10 +165,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2024-07-05T14:21:31.658505Z", - "iopub.status.busy": "2024-07-05T14:21:31.658062Z", - "iopub.status.idle": "2024-07-05T14:21:31.876405Z", - "shell.execute_reply": "2024-07-05T14:21:31.875701Z" + "iopub.execute_input": "2024-07-08T14:19:36.449568Z", + "iopub.status.busy": "2024-07-08T14:19:36.449291Z", + "iopub.status.idle": "2024-07-08T14:19:36.672354Z", + "shell.execute_reply": "2024-07-08T14:19:36.671576Z" } }, "outputs": [