From 997797453d77ffb3f90e90a9cb3ba6a43f10480c Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnku@msu.edu>
Date: Thu, 13 Dec 2018 11:15:50 -0800
Subject: [PATCH] PuReMD-old: tools update in run_sim_mpi.py for larger silica
and water systems.
---
tools/run_sim_puremd.py | 22 ++++++++++++++++++++--
1 file changed, 20 insertions(+), 2 deletions(-)
diff --git a/tools/run_sim_puremd.py b/tools/run_sim_puremd.py
index d1c84dec..cfb2f96c 100644
--- a/tools/run_sim_puremd.py
+++ b/tools/run_sim_puremd.py
@@ -309,8 +309,8 @@ if __name__ == '__main__':
'bilayer_56800', 'bilayer_340800', \
'dna_19733', \
'petn_48256', \
- 'silica_6000', 'silica_72000', 'silica_300000', \
- 'water_6540', 'water_78480', 'water_327000', \
+ 'silica_6000', 'silica_72000', 'silica_300000', 'silica_5832000', \
+ 'water_6540', 'water_78480', 'water_327000', 'water_6540000', \
]
parser = argparse.ArgumentParser(description='Run molecular dynamics simulations on specified data sets.')
@@ -425,6 +425,15 @@ if __name__ == '__main__':
result_header = header_str, result_body_fmt=body_fmt_str,
geo_format=['0'], result_file=result_file,
min_step=min_step, max_step=max_step))
+ if 'water_6540000' in args.data:
+ test_cases.append(
+ TestCase(path.join(data_dir, 'water/water_6540000.geo'),
+ path.join(data_dir, 'water/ffield_acks2.water'),
+ path.join(control_dir, 'parallel_control'),
+ params=params, result_header_fmt=header_fmt_str,
+ result_header = header_str, result_body_fmt=body_fmt_str,
+ geo_format=['0'], result_file=result_file,
+ min_step=min_step, max_step=max_step))
if 'bilayer_56800' in args.data:
test_cases.append(
TestCase(path.join(data_dir, 'bilayer/bilayer_56800.pdb'),
@@ -479,6 +488,15 @@ if __name__ == '__main__':
result_header = header_str, result_body_fmt=body_fmt_str,
geo_format=['0'], result_file=result_file,
min_step=min_step, max_step=max_step))
+ if 'silica_5832000' in args.data:
+ test_cases.append(
+ TestCase(path.join(data_dir, 'silica/silica_5832000.geo'),
+ path.join(data_dir, 'silica/ffield-bio'),
+ path.join(control_dir, 'parallel_control'),
+ params=params, result_header_fmt=header_fmt_str,
+ result_header = header_str, result_body_fmt=body_fmt_str,
+ geo_format=['0'], result_file=result_file,
+ min_step=min_step, max_step=max_step))
if 'petn_48256' in args.data:
test_cases.append(
TestCase(path.join(data_dir, 'petn/petn_48256.pdb'),
--
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