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ntwx for remd (trajcache)
author
Cezary Czaplewski
<czarek@chem.univ.gda.pl>
Sun, 27 Aug 2017 22:17:01 +0000
(
00:17
+0200)
committer
Cezary Czaplewski
<czarek@chem.univ.gda.pl>
Sun, 27 Aug 2017 22:17:01 +0000
(
00:17
+0200)
django_simple/todo/forms.py
patch
|
blob
|
history
django_simple/todo/jobfiles.py
patch
|
blob
|
history
django_simple/todo/templates/details.html
patch
|
blob
|
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django_simple/todo/views.py
patch
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files/matplotlib_hist.py
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diff --git
a/django_simple/todo/forms.py
b/django_simple/todo/forms.py
index
987887b
..
beff582
100644
(file)
--- a/
django_simple/todo/forms.py
+++ b/
django_simple/todo/forms.py
@@
-237,6
+237,8
@@
class TaskForm_remd_a(forms.Form):
help_text='number of replicas')
remd_nstex = forms.IntegerField(label='NSTEX',initial=1000,
help_text='exchange and write trajectory every nstex steps')
help_text='number of replicas')
remd_nstex = forms.IntegerField(label='NSTEX',initial=1000,
help_text='exchange and write trajectory every nstex steps')
+ md_ntwx = forms.IntegerField(label='NTWX',initial=1000,
+ help_text='write trajectory every ntwx steps')
remd_cluter_temp = forms.FloatField(label='TEMPER',
help_text='temperature for cluster analysis',initial=280)
# remd_traj1file = forms.BooleanField(required=False,label='single trajectory file',initial='true')
remd_cluter_temp = forms.FloatField(label='TEMPER',
help_text='temperature for cluster analysis',initial=280)
# remd_traj1file = forms.BooleanField(required=False,label='single trajectory file',initial='true')
diff --git
a/django_simple/todo/jobfiles.py
b/django_simple/todo/jobfiles.py
index
ce0cf44
..
c3484fa
100644
(file)
--- a/
django_simple/todo/jobfiles.py
+++ b/
django_simple/todo/jobfiles.py
@@
-126,7
+126,7
@@
CUTOFF=7.00000 WCORR4=0.00000
type_line = 'reset_vel='+ str(instance.remd_nstex)\
+' nstep='+str(instance.md_nstep)\
+' ntwe='+str(instance.md_ntwe)\
type_line = 'reset_vel='+ str(instance.remd_nstex)\
+' nstep='+str(instance.md_nstep)\
+' ntwe='+str(instance.md_ntwe)\
- +' ntwx='+str(instance.remd_nstex)\
+ +' ntwx='+str(instance.md_ntwx)\
+' dt='+str(instance.md_dt)
if instance.md_lang == 'langevin':
type_line = type_line + ' lang=1 '
+' dt='+str(instance.md_dt)
if instance.md_lang == 'langevin':
type_line = type_line + ' lang=1 '
@@
-142,7
+142,7
@@
CUTOFF=7.00000 WCORR4=0.00000
type_line2 = 'nrep='+str(instance.remd_nrep) \
+' nstex='+str(instance.remd_nstex) \
+' tlist mlist sync nsyn='+str(instance.remd_nstex)\
type_line2 = 'nrep='+str(instance.remd_nrep) \
+' nstex='+str(instance.remd_nstex) \
+' tlist mlist sync nsyn='+str(instance.remd_nstex)\
- +' traj1file rest1file '
+ +' traj1file rest1file TRAJCACHE=200'
if instance.md_start == 'pdbstart':
type_line = type_line + ' preminim cart'
if instance.md_start == 'pdbstart':
type_line = type_line + ' preminim cart'
@@
-270,10
+270,10
@@
CUTOFF=7.00000 WCORR4=0.00000
# write wham & cluster input
with open(instance.jobdirname+'/file_wham.inp','w') as f:
# write wham & cluster input
with open(instance.jobdirname+'/file_wham.inp','w') as f:
- if instance.md_nstep/instance.remd_nstex*nreplicas<=8000:
+ if instance.md_nstep/instance.md_ntwx*nreplicas<=8000:
isampl=1
else:
isampl=1
else:
- isampl=int(instance.md_nstep/instance.remd_nstex*nreplicas/8000)
+ isampl=int(instance.md_nstep/instance.md_ntwx*nreplicas/8000)
if instance.md_pdbref:
f.write('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
if instance.md_pdbref:
f.write('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
@@
-295,7
+295,7
@@
CUTOFF=7.00000 WCORR4=0.00000
for element in tmp1:
f.write('nr=1 temp='+element+' fi=0.0 0.0 0.0 0.0 0.0\n')
f.write('kh= 0.0 Q0=0.0\n')
for element in tmp1:
f.write('nr=1 temp='+element+' fi=0.0 0.0 0.0 0.0 0.0\n')
f.write('kh= 0.0 Q0=0.0\n')
- rec=instance.md_nstep/instance.remd_nstex
+ rec=instance.md_nstep/instance.md_ntwx
f.write('nfile_cx=1 rec_start='+str(rec/10)
+' rec_end='+str(rec)+' totraj='+str(nreplicas)+'\n')
f.write('file_MD000\n')
f.write('nfile_cx=1 rec_start='+str(rec/10)
+' rec_end='+str(rec)+' totraj='+str(nreplicas)+'\n')
f.write('file_MD000\n')
diff --git
a/django_simple/todo/templates/details.html
b/django_simple/todo/templates/details.html
index
b640281
..
6a7f396
100644
(file)
--- a/
django_simple/todo/templates/details.html
+++ b/
django_simple/todo/templates/details.html
@@
-175,10
+175,18
@@
Created {{ task.created_date }}
<div class="col-xs-10">{{ task.md_nstep}}</div>
</li>
<li class="list-group-item task-item">
<div class="col-xs-10">{{ task.md_nstep}}</div>
</li>
<li class="list-group-item task-item">
+ <div class="col-xs-10"> ntwe </div>
+ <div class="col-xs-10">{{ task.md_ntwe}}</div>
+ </li>
+ <li class="list-group-item task-item">
<div class="col-xs-10"> nstex </div>
<div class="col-xs-10">{{ task.remd_nstex}}</div>
</li>
<li class="list-group-item task-item">
<div class="col-xs-10"> nstex </div>
<div class="col-xs-10">{{ task.remd_nstex}}</div>
</li>
<li class="list-group-item task-item">
+ <div class="col-xs-10"> ntwx </div>
+ <div class="col-xs-10">{{ task.md_ntwx}}</div>
+ </li>
+ <li class="list-group-item task-item">
<div class="col-xs-10"> dt </div>
<div class="col-xs-10">{{ task.md_dt}}</div>
</li>
<div class="col-xs-10"> dt </div>
<div class="col-xs-10">{{ task.md_dt}}</div>
</li>
diff --git
a/django_simple/todo/views.py
b/django_simple/todo/views.py
index
6f3a75e
..
2ec8735
100644
(file)
--- a/
django_simple/todo/views.py
+++ b/
django_simple/todo/views.py
@@
-250,6
+250,7
@@
def add_remd(request,task_id):
task.md_start=form.cleaned_data["md_start"]
task.myfile1=form.cleaned_data["file1"]
task.md_pdbref=form.cleaned_data["md_pdbref"]
task.md_start=form.cleaned_data["md_start"]
task.myfile1=form.cleaned_data["file1"]
task.md_pdbref=form.cleaned_data["md_pdbref"]
+ task.md_ntwx=task.remd_nstex
task.md_seq=""
if task.md_start == "pdbstart" or task.md_pdbref:
task.md_seq=""
if task.md_start == "pdbstart" or task.md_pdbref:
@@
-313,6
+314,7
@@
def add_remd_a(request,task_id):
task.md_scal_fric=form.cleaned_data["md_scal_fric"]
task.remd_nrep=form.cleaned_data["remd_nrep"]
task.remd_nstex=form.cleaned_data["remd_nstex"]
task.md_scal_fric=form.cleaned_data["md_scal_fric"]
task.remd_nrep=form.cleaned_data["remd_nrep"]
task.remd_nstex=form.cleaned_data["remd_nstex"]
+ task.md_ntwx=form.cleaned_data["md_ntwx"]
# task.remd_traj1file=form.cleaned_data["remd_traj1file"]
# task.remd_rest1file=form.cleaned_data["remd_rest1file"]
# task.remd_traj1file=form.cleaned_data["remd_traj1file"]
# task.remd_rest1file=form.cleaned_data["remd_rest1file"]
diff --git
a/files/matplotlib_hist.py
b/files/matplotlib_hist.py
index
36b55aa
..
6bf943f
100755
(executable)
--- a/
files/matplotlib_hist.py
+++ b/
files/matplotlib_hist.py
@@
-92,7
+92,7
@@
if ncolumns==14:
yt=rms[r==i]
xt=(s+r*max(s))[r==i]
tt=x[r==i]
yt=rms[r==i]
xt=(s+r*max(s))[r==i]
tt=x[r==i]
- plt.scatter(xt,yt,c=tt,edgecolors='face',s=0.1,cmap=cm.rainbow)
+ plt.scatter(xt,yt,c=tt,edgecolors='face',s=0.1,cmap=cm.rainbow,vmin=Tremd[0],vmax=Tremd[-1])
plt.xlim(0,max(s)+max(s)*max(r))
plt.savefig('remd_step_rms.png')
plt.xlim(0,max(s)+max(s)*max(r))
plt.savefig('remd_step_rms.png')
@@
-102,7
+102,7
@@
x,y,rms= np.loadtxt('file_wham.thermal',usecols=(0,6,4),unpack=True)
plt.clf()
plt.xlabel('bath temperature [K]')
plt.ylabel('heat capacity')
plt.clf()
plt.xlabel('bath temperature [K]')
plt.ylabel('heat capacity')
-plt.xlim(Tremd[1]-10, Tremd[-1]+10)
+plt.xlim(Tremd[0], Tremd[-1])
plt.plot(x,y,'-',color=c)
plt.savefig('remd_cv.png')
plt.plot(x,y,'-',color=c)
plt.savefig('remd_cv.png')