These are the added instructions to run the MoSDeF builds for GOMC a… #45
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…nd the GOMC simulations
| * module_load_command_3 = Add your HPC specific module command here as a string or set as None | ||
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| 4) Run the python build script simbuild.py | ||
| * python simbuild.py |
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Could you use markdown for the python commands like python simbuild.py?
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I thought this would print nice on the github page when you are viewing it though there. If you still want me to change it I can.
| * "full_path_to_GOMC_bin_folder"/GOMC_CPU_NVT +p2 in.conf > out.dat | ||
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| Alternatively, Run the code using the CPU/GPU: | ||
| * "full_path_to_GOMC_bin_folder"/GOMC_GPU_NVT +p2 in.conf > out.dat |
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Same as markdown comment above.
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I thought this would print nice on the github page when you are viewing it though there. If you still want me to change it I can.
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I think it will still look nice with the bullet point. Something like:
"full_path_to_GOMC_bin_folder"/GOMC_GPU_NVT +p2 in.conf > out.dat
Just to distinguish it from the rest of the text. Let me know what you think.
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Sorry I guess I'm confused. I took the format from the mosdef_slitpore/README.md file. Which appeared to print bullet points in the GitHub page when presented as with the '*" symbol. When I preview this example here below it prints a bullet point in preview mode. Do you mean when viewing the hard file and not via GitHub? Or just mean that they should be indented?
Example:
- Change the terminal window directory to the set1 directory (i.e., to mosdef_slitpore/mosdef_slitpore/simulations/nvt-pore/1x1x1.0nm_1-layer/gomc/set1).
- cd ../set1
simulations/adsorption/3x3x1.0nm_3-layer/gomc/build_ads_system/build_Graphene_water.py
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simulations/adsorption/3x3x1.0nm_3-layer/gomc/build_ads_system/build_Graphene_water.py
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… required file and functions in that one file. Changed the GOMC file builders to run off this.
simulations/nvt-pore/1x1x1.0nm_1-layer/gomc/NVT_build/NVT_build_pore_1x1x1.0nm_1-layer.py
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…nimization with water.energy_minimize for all the build files.
….0nm_1-layer/gomc/README.md
This PR contains the modified MoSDeF build files and the modified GOMC run files that work in the new directory structure. Also, there are instructions (Readme) files that walk the user thru how to run the MoSDeF code and the GOMC simulations, which are provided in every major section.