From dbcd2764d06f4bc3828ca0995041a632b731c9de Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Thu, 20 Sep 2018 19:57:38 -0500
Subject: [PATCH] Removed cache in resources
---
mrdna/model/nbPot.py | 3 ---
mrdna/simulate.py | 32 +++++++++++++++++++++++---------
2 files changed, 23 insertions(+), 12 deletions(-)
diff --git a/mrdna/model/nbPot.py b/mrdna/model/nbPot.py
index e744f82..e730a45 100644
--- a/mrdna/model/nbPot.py
+++ b/mrdna/model/nbPot.py
@@ -9,9 +9,6 @@ from mrdna.config import CACHE_DIR
## TODO: clean this file up a bit, make things protected
-_package_cache_dir = get_resource_path("nbPot_cache")
-_package_cache_dir.mkdir(exist_ok=True)
-
_dxParam = -1
def _maxForce(x,u0,maxForce=40):
diff --git a/mrdna/simulate.py b/mrdna/simulate.py
index df93fc4..7494f9b 100644
--- a/mrdna/simulate.py
+++ b/mrdna/simulate.py
@@ -21,7 +21,9 @@ def multiresolution_simulation( model, output_name,
## Round steps up to nearest multiple of output_period, plus 1
coarse_steps = ((coarse_steps+coarse_output_period-1)//coarse_output_period)*coarse_output_period+1
- fine_steps = ((fine_steps+fine_output_period-1)//fine_output_period)*fine_output_period+1
+ fine_steps = ((fine_steps+fine_output_period-1)//fine_output_period)
+ if fine_steps == 1: fine_steps += 1
+ fine_steps = fine_steps*fine_output_period+1
ret = None
d_orig = os.getcwd()
@@ -74,10 +76,16 @@ def multiresolution_simulation( model, output_name,
model._clear_beads()
model._generate_bead_model( 1, 1, local_twist=True, escapable_twist=True )
model.simulate( output_name = output_prefix, num_steps=fine_steps, **simargs )
- try:
- coordinates = readAvgArbdCoords('%s.psf' % output_prefix,'%s.pdb' % output_prefix, '%s.dcd' % full_output_prefix, rmsdThreshold=1)
- except:
- coordinates = readAvgArbdCoords('%s.psf' % output_prefix,'%s.pdb' % output_prefix, '%s.0.dcd' % full_output_prefix, rmsdThreshold=1)
+ if fine_steps <= 2*fine_output_period+1:
+ try:
+ coordinates = readArbdCoords('%s.restart' % full_output_prefix)
+ except:
+ coordinates = readArbdCoords('%s.0.restart' % full_output_prefix)
+ else:
+ try:
+ coordinates = readAvgArbdCoords('%s.psf' % output_prefix,'%s.pdb' % output_prefix, '%s.dcd' % full_output_prefix, rmsdThreshold=1)
+ except:
+ coordinates = readAvgArbdCoords('%s.psf' % output_prefix,'%s.pdb' % output_prefix, '%s.0.dcd' % full_output_prefix, rmsdThreshold=1)
""" Freeze twist """
@@ -87,10 +95,16 @@ def multiresolution_simulation( model, output_name,
model._clear_beads()
model._generate_bead_model( 1, 1, local_twist=True, escapable_twist=False )
model.simulate( output_name = output_prefix, num_steps=fine_steps, **simargs )
- try:
- coordinates = readAvgArbdCoords('%s.psf' % output_prefix,'%s.pdb' % output_prefix, '%s.dcd' % full_output_prefix )
- except:
- coordinates = readAvgArbdCoords('%s.psf' % output_prefix,'%s.pdb' % output_prefix, '%s.0.dcd' % full_output_prefix )
+ if fine_steps <= 2*fine_output_period+1:
+ try:
+ coordinates = readArbdCoords('%s.restart' % full_output_prefix)
+ except:
+ coordinates = readArbdCoords('%s.0.restart' % full_output_prefix)
+ else:
+ try:
+ coordinates = readAvgArbdCoords('%s.psf' % output_prefix,'%s.pdb' % output_prefix, '%s.dcd' % full_output_prefix, rmsdThreshold=1)
+ except:
+ coordinates = readAvgArbdCoords('%s.psf' % output_prefix,'%s.pdb' % output_prefix, '%s.0.dcd' % full_output_prefix, rmsdThreshold=1)
""" Atomic simulation """
--
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