ntwx for remd (trajcache)

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')
+     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')

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)\
-             +' 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 '
@@ -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)\
-             +' traj1file  rest1file '
+             +' traj1file  rest1file TRAJCACHE=200'
 
        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:
-          if instance.md_nstep/instance.remd_nstex*nreplicas<=8000:
+          if instance.md_nstep/instance.md_ntwx*nreplicas<=8000:
               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)+
@@ -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')
-          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')

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"> 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"> 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>           

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_ntwx=task.remd_nstex 
 
              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_ntwx=form.cleaned_data["md_ntwx"]             
 #             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]
-    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')
   
@@ -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.xlim(Tremd[1]-10, Tremd[-1]+10)
+plt.xlim(Tremd[0], Tremd[-1])
 plt.plot(x,y,'-',color=c) 
 plt.savefig('remd_cv.png')