def main():
options = options_desc.parse_args(sys.argv)[0]
pool = Pool()
needy_nodes = pool.where("state == 'grompp-able'")
assert (len(needy_nodes) == len(needy_nodes.multilock())
) # make sure we lock ALL nodes
if (options.solv_model == "tip3p"):
solv_box = "spc216.gro"
solv_fn = "tip3p.itp"
elif (options.solv_model == "tip4p"):
solv_box = "tip4p.gro"
solv_fn = "tip4p.itp"
elif (options.solv_model == "tip4pew"):
solv_box = "tip4p.gro"
solv_fn = "tip4pew.itp"
elif (options.solv_model == "tip5"):
solv_box = "tip5p.gro"
solv_fn = "tip5p.itp"
elif (options.solv_model == "spc"):
solv_box = "spc216.gro"
solv_fn = "spc.itp"
elif (options.solv_model == "spce"):
solv_box = "spc216.gro"
solv_fn = "spce.itp"
elif (
options.solv_model == "acetonitrile"
): # TODO one might change this one to "custom" and let user enter name of template box
solv_box = "acetonitrile.pdb"
msg = "Topology update for acetonitrile is not supported. Proceed?"
if not (userinput(msg, "bool")):
for n in needy_nodes:
n.unlock()
return ("Quit by user.")
# determine maximum length of linears, if any
max_linear = query_linear_length(pool)
# make box and fill with solvent
genbox(pool, max_linear, options.bt,
(options.box_x, options.box_y, options.box_z), solv_box)
# update topology files (add solvent model and ions includes)
if not (options.solv_model == "acetonitrile"):
update_tops(pool, solv_fn)
for n in needy_nodes:
n.state = "em-grompp-able"
zgf_grompp.call_grompp(
n, mdp_file=options.grompp, final_state="em-mdrun-able"
) # re-grompp to get a tpr for energy minimization
n.unlock()
def main():
options = options_desc.parse_args(sys.argv)[0]
pool = Pool()
needy_nodes = pool.where("state == 'em-mdrun-able'")
assert(len(needy_nodes) == len(needy_nodes.multilock())) # make sure we lock ALL nodes
# add ions to simulation boxes
call_genion(pool, options.np, options.pname, options.nn, options.nname, options.random_seed)
for n in needy_nodes:
n.state = "em-grompp-able"
zgf_grompp.call_grompp(n, mdp_file=options.grompp, final_state="em-mdrun-able") # re-grompp to get a tpr for energy minimization
n.unlock()
def main():
options = options_desc.parse_args(sys.argv)[0]
pool = Pool()
needy_nodes = pool.where("state == 'grompp-able'")
assert(len(needy_nodes) == len(needy_nodes.multilock())) # make sure we lock ALL nodes
if(options.solv_model == "tip3p"):
solv_box = "spc216.gro"
solv_fn = "tip3p.itp"
elif(options.solv_model == "tip4p"):
solv_box = "tip4p.gro"
solv_fn = "tip4p.itp"
elif(options.solv_model == "tip4pew"):
solv_box = "tip4p.gro"
solv_fn = "tip4pew.itp"
elif(options.solv_model == "tip5"):
solv_box = "tip5p.gro"
solv_fn = "tip5p.itp"
elif(options.solv_model == "spc"):
solv_box = "spc216.gro"
solv_fn = "spc.itp"
elif(options.solv_model == "spce"):
solv_box = "spc216.gro"
solv_fn = "spce.itp"
elif(options.solv_model == "acetonitrile"): # TODO one might change this one to "custom" and let user enter name of template box
solv_box = "acetonitrile.pdb"
msg = "Topology update for acetonitrile is not supported. Proceed?"
if not(userinput(msg, "bool")):
for n in needy_nodes:
n.unlock()
return("Quit by user.")
# determine maximum length of linears, if any
max_linear = query_linear_length(pool)
# make box and fill with solvent
genbox(pool, max_linear, options.bt, (options.box_x, options.box_y, options.box_z), solv_box)
# update topology files (add solvent model and ions includes)
if not(options.solv_model == "acetonitrile"):
update_tops(pool, solv_fn)
for n in needy_nodes:
n.state = "em-grompp-able"
zgf_grompp.call_grompp(n, mdp_file=options.grompp, final_state="em-mdrun-able") # re-grompp to get a tpr for energy minimization
n.unlock()
def main():
options = options_desc.parse_args(sys.argv)[0]
pool = Pool()
needy_nodes = pool.where("state == 'em-mdrun-able'")
assert (len(needy_nodes) == len(needy_nodes.multilock())
) # make sure we lock ALL nodes
# add ions to simulation boxes
call_genion(pool, options.np, options.pname, options.nn, options.nname,
options.random_seed)
for n in needy_nodes:
n.state = "em-grompp-able"
zgf_grompp.call_grompp(
n, mdp_file=options.grompp, final_state="em-mdrun-able"
) # re-grompp to get a tpr for energy minimization
n.unlock()
def process(node, options):
cmd1 = ["mdrun"]
if(node.state == "em-mdrun-able"):
cmd1 += ["-s", "../../"+node.tpr_fn]
cmd1 += ["-c", "../../"+node.pdb_fn]
cmd1 += ["-o", "../../"+node.dir+"/em.trr"]
cmd1 += ["-e", "../../"+node.dir+"/em.edr"]
cmd1 += ["-g", "../../"+node.dir+"/em.log"]
elif(node.state in ('rerun-able-converged','rerun-able-not-converged')):
cmd1 += ["-s", "../../"+node.dir+"/rerun_me.tpr"]
cmd1 += ["-rerun", "../../"+node.dir+"/rerun_me.trr"]
cmd1 += ["-o", "../../"+node.dir+"/rerun.trr"]
cmd1 += ["-e", "../../"+node.dir+"/rerun.edr"]
cmd1 += ["-g", "../../"+node.dir+"/rerun.log"]
else:
cmd1 += ["-s", "../../"+node.tpr_fn]
cmd1 += ["-o", "../../"+node.trr_fn]
cmd1 += ["-c", "../../"+node.dir+"/outfile.pdb"]
cmd1 += ["-append", "-cpi", "state.cpt"] # continue previouly state, if exists
if(options.npme != -1):
cmd1 += ["-npme", str(options.npme)]
if(options.nt != 0):
cmd1 += ["-nt", str(options.nt)]
if(options.reprod):
cmd1 += ["-reprod"]
if(options.pd):
cmd1 += ["-pd"]
# do parallel job if preferred
if(not options.seq):
if(call(["which","mdrun_mpi"])==0):
cmd1[0] = "mdrun_mpi"
if(call(["which","mpiexec"])==0):
cmd1 = ["mpiexec", "-np", str(options.np)] + cmd1
if(not options.seq and str(options.pbs) == "mpiexec" and call(["which","mpiexec"])==0):
cmd1 = ["mpiexec", "-np", str(options.np)] + cmd1
if(not options.seq and str(options.pbs) == "aprun"):
cmd1 = ["aprun", "-n", str(options.np)] + cmd1
## use mpiexec and mdrun_mpi if available
#if(not options.seq and call(["which","aprun"])==0):
# if(call(["which","mdrun_mpi"])==0):
# cmd1[0] = "mdrun_mpi"
# cmd1 = ["aprun", "-n", str(options.np)] + cmd1
#http://stackoverflow.com/questions/4554767/terminating-subprocess-in-python
#alternative
#p = Popen(...)
#pp = psutil.Process(p.pid)
#for child in pp.get_children():
# child.send_signal(signal.SIGINT)
#ensure, that childprocess dies when parent dies. Alternative: write own signal-handler e.g for atexit-module
#http://stackoverflow.com/questions/1884941/killing-the-child-processes-with-the-parent-process
implant_bomb = None
try:
import ctypes
libc = ctypes.CDLL('libc.so.6')
PR_SET_PDEATHSIG = 1; TERM = 15
implant_bomb = lambda: libc.prctl(PR_SET_PDEATHSIG, TERM)
except:
warn("Child process might live on when parent gets terminated (feature requires python 2.6).")
print("Calling: %s"%" ".join(cmd1))
check_call(cmd1, cwd=node.dir, preexec_fn=implant_bomb)
# if we were just minimizing, we go back to grompp-able now
if(node.state == "em-mdrun-able"):
node.state = "grompp-able"
return
# if we were just rerunnning, we go back to original state now
if(node.state in ('rerun-able-converged','rerun-able-not-converged')):
node.state = node.state.rsplit("rerun-able-", 1)[1]
return
if(node.has_restraints and not options.multistart):
# check for convergence
converged = conv_check_gelman_rubin(node)
else:
# stow away sampling data
converged = False
os.remove(node.dir+"/state.cpt")
for fn in [node.dir+"/outfile.pdb",node.trr_fn, node.dir+"/ener.edr", node.dir+"/md.log"]:
archive_file(fn, node.extensions_counter)
# check if user wants to delete files except pdb
try:
if (node.save_mode == "pdb"):
# delete all files except pdb and start files
for fn in os.listdir(node.dir):
if(re.match(".+.pdb",fn)==None
and re.match("[^#].+.mdp",fn)==None
and re.match(".+.txt",fn)==None
and re.match("[^#].+.tpr",fn)==None
and re.match(".+.top",fn)==None
and fn!="lock"):
os.remove(node.dir+"/"+str(fn))
except AttributeError:
pass
# decide what to do next
if(converged):
node.state = "converged"
elif(node.extensions_counter >= node.extensions_max):
if(node.has_restraints and not options.multistart):
node.state = "not-converged"
else:
# if user wants to keep everthing we at merge trajectorie and edr files
# and delete backups
try:
if (node.save_mode == "complete"):
# merge sampling trajectories
trr_fns = sorted([ fn for fn in os.listdir(node.dir) if re.match("[^#].+run\d+.trr", fn) ])
cmd2 = ["trjcat", "-f"]
cmd2 += trr_fns
cmd2 += ["-o", "../../"+node.trr_fn, "-cat"]
print("Calling: %s"%" ".join(cmd2))
check_call(cmd2, cwd=node.dir)
# merge edr files
get_merged_edr(node)
# delete backups, assuming each backup file starts with '#'
for fn in os.listdir(node.dir):
if(re.match("#.+",fn)):
os.remove(node.dir+"/"+str(fn))
except AttributeError:
pass
# in either case, save as ready node
node.state = "ready"
else:
node.extensions_counter += 1
node.state = "mdrun-able" # actually it should still be in this state
if(node.has_restraints and not options.multistart):
cmd0 = ["tpbconv", "-s", node.tpr_fn, "-o", node.tpr_fn, "-extend", str(node.extensions_length)]
print("Calling: %s"%" ".join(cmd0))
check_call(cmd0) # tell Gromacs to extend the tpr file for another round
else:
node.state = "grompp-able"
zgf_grompp.call_grompp(node) # re-grompp to obtain new random impulse