variable serialization

[qcg-portal.git] / qcg / utils.py

diff --git a/qcg/utils.py b/qcg/utils.py
index da8f83c..c6453e9 100644 (file)
--- a/qcg/utils.py
+++ b/qcg/utils.py
@@ -73,9 +73,9 @@ def generate_md_inputfile(params):
     # Dane kontrolne obliczen
     md_input.append('SEED=-3059743 PDBREF ONE_LETTER MD EXTCONF RESCALE_MODE=2')
     ctl_data='nstep='+str(params['nstep'])+' ntwe='+str(params['ntwe'])
-    ctl_data+=' ntwx='+str(params['ntwx'])+' dt='+str(params['dt'])+' damax='+str(params['damax'])+'lang=0 tbf'
+    ctl_data+=' ntwx='+str(params['ntwx'])+' dt='+str(params['dt'])+' damax='+str(params['damax'])+'lang=1 scal_fric=0.01'
     md_input.append('{:<79}&'.format(ctl_data))
-    md_input.append('tau_bath=1.0 t_bath=300 reset_vel=10000 respa ntime_split=1 maxtime_split=512')
+    md_input.append('tau_bath=1.0 t_bath=300 reset_vel=0 respa ntime_split=1 maxtime_split=512 mdpdb')
     # Paramatry pól siłowych
     if params['force_field'] == 'GAB':
         # Wagi pola GAB
@@ -141,6 +141,24 @@ def to_job_desc(params, proxy):
     if params['watch_output']:
         desc.set_watch_output(params['watch_output'], params['watch_output_pattern'])
 
+    przemytnik = params['env_variables']
+    if params['force_field']:
+        przemytnik.append([u'UNRESPORTAL_FORCEFIELD',params['force_field']])
+    if params['sequence']:
+        przemytnik.append([u'UNRESPORTAL_SEQUENCE',params['sequence']])
+    if params['pdb_file']:
+        przemytnik.append([u'UNRESPORTAL_PDBFILE',params['pdb_file']])
+    if params['nstep']:
+        przemytnik.append([u'UNRESPORTAL_NSTEP',params['nstep']])
+    if params['ntwe']:
+        przemytnik.append([u'UNRESPORTAL_NTWE',params['ntwe']])
+    if params['ntwx']:
+        przemytnik.append([u'UNRESPORTAL_NTWX',params['ntwx']])
+    if params['dt']:
+        przemytnik.append([u'UNRESPORTAL_DT',params['dt']])
+    if params['damax']:
+        przemytnik.append([u'UNRESPORTAL_DAMAX',params['damax']])
+    setattr(desc, 'env_variables', przemytnik)
     # TODO monitoring
     
     return desc
@@ -155,7 +173,7 @@ def to_form_data(xml):
     desc.xml_description = xml
 
     direct_map = ('env_variables', 'executable', 'arguments', 'note', 'grant', 'hosts', 'properties', 'queue', 'procs',
-                  'wall_time', 'memory', 'memory_per_slot', 'modules', 'input', 'stage_in', 'native', 'persistent')
+                  'wall_time', 'modules', 'input', 'stage_in', 'native', 'persistent')
 
     params = {}
     for name in direct_map:
@@ -193,7 +211,28 @@ def to_form_data(xml):
         else:
             params['postprocess_type'] = JobDescriptionForm.Process.CMD
             params['postprocess_cmd'] = desc.postprocess
-
+    if desc.memory:
+        params['memory'] = int(desc.memory)
+    if desc.memory_per_slot:
+        params['memory_per_slot'] = int(desc.memory_per_slot)
+
+    for item in desc.env_variables:
+        if item[0] == u'UNRESPORTAL_FORCEFIELD':
+            params['force_field'] = item[1]
+        if item[0] == u'UNRESPORTAL_SEQUENCE':
+            params['sequence'] = item[1]
+        if item[0] == u'UNRESPORTAL_PDBFILE':
+            params['pdb_file'] = item[1]
+        if item[0] == u'UNRESPORTAL_NSTEP':
+            params['nstep'] = item[1]
+        if item[0] == u'UNRESPORTAL_NTWE':
+            params['ntwe'] = item[1]
+        if item[0] == u'UNRESPORTAL_NTWX':
+            params['ntwx'] = item[1]
+        if item[0] == u'UNRESPORTAL_DT':
+            params['dt'] = item[1]
+        if item[0] == u'UNRESPORTAL_DAMAX':
+            params['damax'] = item[1]
     return params