From 647e875ae19d11fbd017783e83230cbb7c5582d1 Mon Sep 17 00:00:00 2001
From: s2123329 <h.pollak@sms.ed.ac.uk>
Date: Wed, 15 May 2024 16:30:46 +0100
Subject: [PATCH] Update siminp for d-spacing

---
 package/ClayCode/core/parsing.py             | 17 ++++++++++-------
 package/ClayCode/data/data/MDP/defaults.yaml |  5 +++--
 package/ClayCode/siminp/writer.py            |  8 ++++----
 3 files changed, 17 insertions(+), 13 deletions(-)

diff --git a/package/ClayCode/core/parsing.py b/package/ClayCode/core/parsing.py
index 86d528e..f2701cd 100644
--- a/package/ClayCode/core/parsing.py
+++ b/package/ClayCode/core/parsing.py
@@ -608,13 +608,16 @@ def wrapper(self: _Args, enumerate_duplicates=False):
                                 else:
                                     if self.data[key].suffix != "":
                                         self.data[key] = self.data[key].parent
-                                    path_list.extend(
-                                        [
-                                            self.data[key]
-                                            / path.relative_to(path.cwd()),
-                                            self.data[key] / v,
-                                        ]
-                                    )
+                                    try:
+                                        path_list.extend(
+                                            [
+                                                self.data[key]
+                                                / path.relative_to(path.cwd()),
+                                                self.data[key] / v,
+                                            ]
+                                        )
+                                    except ValueError:
+                                        path_list.extend([self.data[key] / v])
                             for path_option in path_list:
                                 try:
                                     path_option = File(path_option, check=True)
diff --git a/package/ClayCode/data/data/MDP/defaults.yaml b/package/ClayCode/data/data/MDP/defaults.yaml
index 898879a..bc901e1 100644
--- a/package/ClayCode/data/data/MDP/defaults.yaml
+++ b/package/ClayCode/data/data/MDP/defaults.yaml
@@ -931,7 +931,7 @@ NVT:
   tcoupl: "nose-hoover"
   constraints: "h-bonds"
   constraint-algorithm: "lincs"
-D-SPACE:
+D_SPACE:
   dt: "0.001"
   integrator: "md"
   tinit: "0"
@@ -948,7 +948,7 @@ D-SPACE:
   tau-p: "1.0"
   tau-t: "0.2"
   tc-grps: "system"
-  tcoupl: "nose-hoover"
+  tcoupl: "berendsen"
 EM:
   constraints: "none"
   emstep: "0.0005"
@@ -1149,3 +1149,4 @@ GENION:
   wall-ewald-zfac: ""
   wall-r-linpot: ""
   wall-type: ""
+  constraint_algorithm: ""
diff --git a/package/ClayCode/siminp/writer.py b/package/ClayCode/siminp/writer.py
index bcce9cd..a75055a 100644
--- a/package/ClayCode/siminp/writer.py
+++ b/package/ClayCode/siminp/writer.py
@@ -150,14 +150,14 @@ def get_run_path(self, filename: PathOrStr):
                 out_part = self.odir
             relpath = list(out_part.parts)[-1]
             new_rdir = []
-            for rd in self.run_path.parts[1:]:
+            for rd in self.run_path.parts:
                 if rd not in out_part.parts:
                     new_rdir.append(rd)
                 else:
                     relpath = Path(*out_part.parts[out_part.parts.index(rd) :])
                     break
-            if len(new_rdir) != 0:
-                new_rdir.insert(0, "/")
+            # if len(new_rdir) != 0:
+            #     new_rdir.insert(0, "/")
             new_rdir = Path(*new_rdir, relpath)
             return new_rdir / rel_filename
         else:
@@ -789,7 +789,6 @@ def get_run_command(self, gmx_alias="gmx", max_run=10, mdrun_prms=None):
             mdrun_prms_str = "".join(
                 [f" -{k} {v}" for k, v in mdrun_prms.items()]
             )
-        mdrun_prms_str
         with open(DSPACE_RUN_SCRIPT, "r") as dspace_run_file:
             dspace_run_string = dspace_run_file.read()
         dspace_run_string = substitute_kwds(
@@ -1087,6 +1086,7 @@ def write_runs(
         mdrun_prms: Optional[Union[MDPFile, File, str]] = None,
         shell: Optional[str] = None,
         header: Optional[str] = None,
+        gmx_version: Optional[int] = None,
         **kwargs,
     ):
         """Write the run script for the run sequence.