def sim(inp):
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
#cpc.util.plugin.testCommand("trjcat -version")
#cpc.util.plugin.testCommand("eneconv -version")
#cpc.util.plugin.testCommand("gmxdump -version")
return
pers=cpc.dataflow.Persistence(os.path.join(inp.getPersistentDir(),
"persistent.dat"))
inputs = ['tpr','plumed']
outputs = [ 'COLVAR', 'bias']
running=0
if(pers.get("running")):
running=pers.get("running")
it=iterate.iterations(inp, inputs, outputs, pers)
out=inp.getFunctionOutput()
for i in range(running, it.getN()):
instName="replica_%d"%i
out.addInstance(instName, "replica")
it.connect(out, i, instName)
running+=1
pers.set("running", running)
pers.write()
log.debug("----------------------EXITING THE SIM FUNCTION-------------------")
return out
def mdruns(inp):
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("trjcat -version")
cpc.util.plugin.testCommand("eneconv -version")
cpc.util.plugin.testCommand("gmxdump -version")
return
pers=cpc.dataflow.Persistence(os.path.join(inp.getPersistentDir(),
"persistent.dat"))
inputs = ['tpr','priority','cmdline_options','resources','plumed']
outputs = [ 'conf', 'xtc', 'trr', 'edr','COLVAR', 'HILLS', 'bias']
running=0
if(pers.get("running")):
running=pers.get("running")
it=iterate.iterations(inp, inputs, outputs, pers)
out=inp.getFunctionOutput()
for i in range(running, it.getN()):
instName="mdrun_%d"%i
out.addInstance(instName, "mdrun")
it.connect(out, i, instName)
running+=1
pers.set("running", running)
pers.write()
return out
def mdruns(inp):
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("trjcat -version")
cpc.util.plugin.testCommand("eneconv -version")
cpc.util.plugin.testCommand("gmxdump -version")
return
pers=cpc.dataflow.Persistence(os.path.join(inp.getPersistentDir(),
"persistent.dat"))
inputs = ['tpr','priority','cmdline_options','resources','plumed']
outputs = [ 'conf', 'xtc', 'trr', 'edr','COLVAR', 'HILLS', 'bias']
running=0
if(pers.get("running")):
running=pers.get("running")
it=iterate.iterations(inp, inputs, outputs, pers)
out=inp.getFunctionOutput()
for i in range(running, it.getN()):
instName="mdrun_%d"%i
out.addInstance(instName, "mdrun")
it.connect(out, i, instName)
running+=1
pers.set("running", running)
pers.write()
return out
def grompp_mdruns(inp):
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("grompp -version")
return
pers=cpc.dataflow.Persistence(os.path.join(inp.getPersistentDir(),
"persistent.dat"))
grompp_inputs = ['mdp','top','conf', 'ndx', 'settings', 'include' ]
mdrun_inputs = [ 'priority', 'cmdline_options', 'resources', 'plumed']
inputs = grompp_inputs + mdrun_inputs
grompp_outputs = [ 'tpr' ]
mdrun_outputs = [ 'conf', 'xtc', 'trr', 'edr','COLVAR','HILLS','bias' ]
outputs = grompp_outputs + mdrun_outputs
running=0
if(pers.get("running")):
running=pers.get("running")
it=iterate.iterations(inp, inputs, outputs, pers)
out=inp.getFunctionOutput()
for i in range(running, it.getN()):
gromppInstName="grompp_%d"%i
mdrunInstName="mdrun_%d"%i
try:
out.addInstance(gromppInstName, "gromacs::grompp")
except:
log.debug("Error: You must import the gromacs module to use this function.")
out.addInstance(mdrunInstName, "mdrun")
out.addConnection('%s:out.tpr'%gromppInstName,
'%s:in.tpr'%mdrunInstName)
it.connectOnly(grompp_inputs, grompp_outputs, out, i, gromppInstName)
it.connectOnly(mdrun_inputs, mdrun_outputs, out, i, mdrunInstName)
running+=1
pers.set("running", running)
pers.write()
return out
def grompp_mdruns(inp):
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("grompp -version")
return
pers=cpc.dataflow.Persistence(os.path.join(inp.getPersistentDir(),
"persistent.dat"))
grompp_inputs = ['mdp','top','conf', 'ndx', 'settings', 'include' ]
mdrun_inputs = [ 'priority', 'cmdline_options', 'resources', 'plumed']
inputs = grompp_inputs + mdrun_inputs
grompp_outputs = [ 'tpr' ]
mdrun_outputs = [ 'conf', 'xtc', 'trr', 'edr','COLVAR','HILLS','bias' ]
outputs = grompp_outputs + mdrun_outputs
running=0
if(pers.get("running")):
running=pers.get("running")
it=iterate.iterations(inp, inputs, outputs, pers)
out=inp.getFunctionOutput()
for i in range(running, it.getN()):
gromppInstName="grompp_%d"%i
mdrunInstName="mdrun_%d"%i
try:
out.addInstance(gromppInstName, "gromacs::grompp")
except:
log.debug("Error: You must import the gromacs module to use this function.")
out.addInstance(mdrunInstName, "mdrun")
out.addConnection('%s:out.tpr'%gromppInstName,
'%s:in.tpr'%mdrunInstName)
it.connectOnly(grompp_inputs, grompp_outputs, out, i, gromppInstName)
it.connectOnly(mdrun_inputs, mdrun_outputs, out, i, mdrunInstName)
running+=1
pers.set("running", running)
pers.write()
return out
