def grompp_mdruns(inp):
cmdnames = cmds.GromacsCommands()
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("%s -version" % cmdnames.grompp)
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']
inputs = grompp_inputs + mdrun_inputs
grompp_outputs = [ 'tpr' ]
mdrun_outputs = [ 'conf', 'xtc', 'trr', 'edr', 'log' ]
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 xrange(running, it.getN()):
gromppInstName="grompp_%d"%i
mdrunInstName="mdrun_%d"%i
out.addInstance(gromppInstName, "grompp")
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 mdruns(inp):
cmdnames = cmds.GromacsCommands()
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("%s -version" % cmdnames.trjcat)
cpc.util.plugin.testCommand("%s -version" % cmdnames.eneconv)
cpc.util.plugin.testCommand("%s -version" % cmdnames.gmxdump)
return
pers=cpc.dataflow.Persistence(os.path.join(inp.getPersistentDir(),
"persistent.dat"))
inputs = ['tpr','priority','cmdline_options','resources']
outputs = [ 'conf', 'xtc', 'trr', 'edr', 'log' ]
running=0
if(pers.get("running")):
running=pers.get("running")
it=iterate.iterations(inp, inputs, outputs, pers)
out=inp.getFunctionOutput()
for i in xrange(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 grompps(inp):
cmdnames = cmds.GromacsCommands()
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("%s -version" % cmdnames.grompp)
return
pers=cpc.dataflow.Persistence(os.path.join(inp.getPersistentDir(),
"persistent.dat"))
inputs = ['mdp','top','conf', 'ndx', 'settings', 'include']
outputs = [ 'tpr' ]
running=0
if(pers.get("running")):
running=pers.get("running")
it=iterate.iterations(inp, inputs, outputs, pers)
out=inp.getFunctionOutput()
for i in xrange(running, it.getN()):
instName="grompp_%d"%i
out.addInstance(instName, "grompp")
it.connect(out, i, instName)
out.addConnection("%s:out.tpr"%instName, "self:ext_out.tpr[%d]"%i)
running+=1
pers.set("running", running)
pers.write()
return out
def grompp_mdruns(inp):
cmdnames = cmds.GromacsCommands()
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("%s -version" % cmdnames.grompp)
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']
inputs = grompp_inputs + mdrun_inputs
grompp_outputs = ['tpr']
mdrun_outputs = ['conf', 'xtc', 'trr', 'edr', 'log']
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 xrange(running, it.getN()):
gromppInstName = "grompp_%d" % i
mdrunInstName = "mdrun_%d" % i
out.addInstance(gromppInstName, "grompp")
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 mdruns(inp):
cmdnames = cmds.GromacsCommands()
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("%s -version" % cmdnames.trjcat)
cpc.util.plugin.testCommand("%s -version" % cmdnames.eneconv)
cpc.util.plugin.testCommand("%s -version" % cmdnames.gmxdump)
return
pers = cpc.dataflow.Persistence(
os.path.join(inp.getPersistentDir(), "persistent.dat"))
inputs = ['tpr', 'priority', 'cmdline_options', 'resources']
outputs = ['conf', 'xtc', 'trr', 'edr', 'log']
running = 0
if (pers.get("running")):
running = pers.get("running")
it = iterate.iterations(inp, inputs, outputs, pers)
out = inp.getFunctionOutput()
for i in xrange(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 grompps(inp):
cmdnames = cmds.GromacsCommands()
if inp.testing():
# if there are no inputs, we're testing wheter the command can run
cpc.util.plugin.testCommand("%s -version" % cmdnames.grompp)
return
pers = cpc.dataflow.Persistence(
os.path.join(inp.getPersistentDir(), "persistent.dat"))
inputs = ['mdp', 'top', 'conf', 'ndx', 'settings', 'include']
outputs = ['tpr']
running = 0
if (pers.get("running")):
running = pers.get("running")
it = iterate.iterations(inp, inputs, outputs, pers)
out = inp.getFunctionOutput()
for i in xrange(running, it.getN()):
instName = "grompp_%d" % i
out.addInstance(instName, "grompp")
it.connect(out, i, instName)
out.addConnection("%s:out.tpr" % instName, "self:ext_out.tpr[%d]" % i)
running += 1
pers.set("running", running)
pers.write()
return out