new force field option

[django_unres.git] / django_simple / todo / jobfiles.py

diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py
index 69c809e..ce0cf44 100644 (file)
--- a/django_simple/todo/jobfiles.py
+++ b/django_simple/todo/jobfiles.py
@@ -32,7 +32,7 @@ def write_on_task_save(sender, instance, **kwargs):
    if instance.ready and not instance.done and instance.running==0:
      if (not os.path.isdir(instance.jobdirname)):
         os.mkdir(instance.jobdirname)
-     os.chdir(instance.jobdirname)
+#     os.chdir(instance.jobdirname)
  
 
 
@@ -41,14 +41,23 @@ def write_on_task_save(sender, instance, **kwargs):
 #wrapper = textwrap.TextWrapper(width=70)
 #word_list = wrapper.wrap(text=md.substitute(nstep=str(nstep)))
 
-     w="""WSC=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954              &
+     if  instance.unres_ff =='E0LL2Y':
+      w="""WSC=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954              &
 WSCLOC=0.10554 WTOR=1.34316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000        &
 WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000    &
 WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.25                                        &
 CUTOFF=7.00000 WCORR4=0.00000
 """
+     else:
+      w="""WSC=0.82686 WSCP=0.96947 WELEC=0.79373 WBOND=1.00000 WANG=0.46542              &
+WSCLOC=0.07969 WTOR=0.81684 WTORD=0.67806 WCORRH=0.00000 WCORR5=0.00000        &
+WCORR6=0.00000 WEL_LOC=0.71100 WTURN3=2.30298 WTURN4=0.86517 WTURN6=0.00000    &
+WSCCOR=0.14577 WVDWPP=0.17781 WHPB=1.00000 WSCP14=0.00000                      &
+CUTOFF=7.00000 WCORR4=0.00000
+"""
+     
 
-     with open('file.inp','w') as f:
+     with open(instance.jobdirname+'/file.inp','w') as f:
        f.write(instance.name + ' UNRES server job'+ '\n')
 
        if instance.type == 'min' :
@@ -205,10 +214,19 @@ CUTOFF=7.00000 WCORR4=0.00000
        
         
      if instance.type == 'min':
-      shutil.copy('../files/pbs.csh','.')
+      os.chdir(instance.jobdirname)
+      if  instance.unres_ff =='E0LL2Y':
+        shutil.copy('../files/pbs.csh','.')
+      else:
+        shutil.copy('../files/pbs_new.csh','pbs.csh')
       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+      os.chdir('..')
      elif instance.type == 'md':
-      f1 = open('../files/pbs_md.csh', 'r')
+      os.chdir(instance.jobdirname)
+      if  instance.unres_ff =='E0LL2Y':
+        f1 = open('../files/pbs_md.csh', 'r')
+      else:
+        f1 = open('../files/pbs_md_new.csh', 'r') 
       f2 = open('pbs.csh', 'w')
       for line in f1:
            f2.write(line.replace('$dimen3',str(dimen3) ))
@@ -221,10 +239,11 @@ CUTOFF=7.00000 WCORR4=0.00000
       f1.close()
 
       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)      
+      os.chdir('..')
      else:
+# instance.type == 'remd'
       tmp1=json.loads(instance.remd_multi_m)
       nreplicas=sum(map(int, tmp1))
-      
 # hardcoded for 4 core nodes with FGPROC=2
       nodes=int(nreplicas*2/4)
       reszta = nreplicas*2-nodes*4
@@ -233,19 +252,24 @@ CUTOFF=7.00000 WCORR4=0.00000
       else:
         pbs = '#PBS -l nodes='+str(nodes)+':ppn=4+1:ppn='+str(reszta)
 
-      f1 = open('../files/pbs8.csh', 'r')
+      os.chdir(instance.jobdirname)
+      if  instance.unres_ff =='E0LL2Y':
+        f1 = open('../files/pbs8.csh', 'r')
+      else:
+        f1 = open('../files/pbs8_new.csh', 'r')
       f2 = open('pbs8.csh', 'w')
       for line in f1:
           if '#PBS -l nodes=4:ppn=4' in line:
            f2.write(line.replace('#PBS -l nodes=4:ppn=4', pbs))
           else:
            tmp1=json.loads(instance.remd_multi_t)
-           f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'"'))
+           f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'" '+str(nreplicas)))
       f1.close()
-      f2.close()  
+      f2.close()
+      os.chdir('..')  
 
 # write wham & cluster input
-      with open('file_wham.inp','w') as f:
+      with open(instance.jobdirname+'/file_wham.inp','w') as f:
           if instance.md_nstep/instance.remd_nstex*nreplicas<=8000:
               isampl=1
           else:
@@ -280,7 +304,7 @@ CUTOFF=7.00000 WCORR4=0.00000
              f.write('plik.pdb\n')
 
            
-      with open('file_cluster.inp','w') as f:
+      with open(instance.jobdirname+'/file_cluster.inp','w') as f:
           f.write(instance.name + ' UNRES server job'+ '\n')
           f.write('nres='+str(len(seq))
              +' one_letter rescale=2 PRINT_CART PDBOUT=1 iopt=1'
@@ -289,11 +313,12 @@ CUTOFF=7.00000 WCORR4=0.00000
           for i in range(0,len(seq),80):
              f.write(seq[i:i+80]+'\n')
           f.write(write_ssbond(instance.ssbond))
-        
+      
+      os.chdir(instance.jobdirname)  
       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+      os.chdir('..')
      
      print ret_code.stdout.readlines()
-     os.chdir('..')
      logger.warning("Dir \"%s\" has been saved." % instance.jobdirname)
      
 @receiver(post_delete, sender=Task)