def main():
options = options_desc.parse_args(sys.argv)[0]
pool = Pool()
needy_nodes = pool.where("state == 'merge-able'").multilock()
if(len(needy_nodes) == 0):
return
# find out about trr time step
dt = 0
nodeDir = needy_nodes[0].dir.split('/')[-1]
for fn in os.listdir(needy_nodes[0].dir):
if re.match("^"+nodeDir+".+run\d+\.trr", fn):
trr = TrrFile(needy_nodes[0].dir+"/"+fn)
dt = trr.first_frame.next().t - trr.first_frame.t
trr.close()
break
# dt is sometimes noisy in the final digits (three digits is femtosecond step = enough)
dt = np.around(dt, decimals=3)
for n in needy_nodes:
if(options.trr):
# merge sampling trajectories
trr_fns = sorted([ fn for fn in os.listdir(n.dir) if re.match("[^#].+run\d+.trr", fn) ])
cmd = ["trjcat", "-f"]
cmd += trr_fns
cmd += ["-o", "../../"+n.trr_fn, "-cat"]
print("Calling: %s"%" ".join(cmd))
check_call(cmd, cwd=n.dir)
if(options.edr):
# merge edr files
# get list of edr-files
edr_fnames = sorted([n.dir+"/"+fn for fn in os.listdir(n.dir) if re.match("[^#].+run\d+.edr", fn)])
assert( len(edr_fnames) == n.extensions_counter+1 )
assert( len(edr_fnames) == n.extensions_max+1 )
time_offset = n.sampling_length+dt
for edr_fn in edr_fnames[1:]:
# adapt edr starting times
cmd = ["eneconv", "-f", edr_fn, "-o", edr_fn, "-settime"]
print("Calling: "+(" ".join(cmd)))
p = Popen(cmd, stdin=PIPE)
p.communicate(input=(str(time_offset)+"\n"))
assert(p.wait() == 0)
time_offset += n.extensions_length+dt
# concatenate edr files with adapted starting times
cmd = ["eneconv", "-f"] + edr_fnames + ["-o", n.dir+"/ener.edr"]
print("Calling: "+(" ".join(cmd)))
p = Popen(cmd)
retcode = p.wait()
assert(retcode == 0)
needy_nodes.unlock()
def check_output(cmd):
print("\n" + '#'*(len(cmd)+13) + "\n# Running: " + cmd + " #\n" + '#'*(len(cmd)+13) +"\n")
tmp_fn = tempfile.mktemp()
# The pipe to tee hides the exit-status of cmd, but its save in $PIPESTATUS
cmd += " | tee "+tmp_fn+" ; exit $PIPESTATUS"
# Debian's default shell is Dash, which does not support $PIPESTATUS
check_call(cmd, shell=True, executable="/bin/bash")
output = open(tmp_fn).read()
os.remove(tmp_fn)
return(output)
def check_output(cmd):
print("\n" + '#' * (len(cmd) + 13) + "\n# Running: " + cmd + " #\n" + '#' *
(len(cmd) + 13) + "\n")
tmp_fn = tempfile.mktemp()
# The pipe to tee hides the exit-status of cmd, but its save in $PIPESTATUS
cmd += " | tee " + tmp_fn + " ; exit $PIPESTATUS"
# Debian's default shell is Dash, which does not support $PIPESTATUS
check_call(cmd, shell=True, executable="/bin/bash")
output = open(tmp_fn).read()
os.remove(tmp_fn)
return (output)
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
def main():
options = options_desc.parse_args(sys.argv)[0]
if options.common_filename:
options.molecule = options.common_filename + ".pdb"
options.presampling = options.common_filename + ".trr"
options.internals = options.common_filename + ".int"
options.grompp = options.common_filename + ".mdp"
options.topology = options.common_filename + ".top"
options.index = options.common_filename + ".ndx"
print("Options:\n%s\n" % pformat(eval(str(options))))
assert path.exists(options.molecule)
assert path.exists(options.presampling)
assert path.exists(options.internals)
assert path.exists(options.grompp)
assert path.exists(options.topology)
# TODO: what if there is no index-file? (make_ndx)
assert path.exists(options.index)
assert "MOI" in gromacs.read_index_file(options.index), "group MOI should be defined in index file"
# checks e.g. if the mdp-file looks good
mdp_options = gromacs.read_mdp_file(options.grompp)
# options we cannot fix
for ref_t in re.findall("[0-9]+", mdp_options["ref_t"]):
assert int(ref_t) == options.temperature, "temperature in mdp file does not match ZIBgridfree temperature"
# TODO drop options.temperature and get temperature directly from mdp file... ask again if temperature is above 310K
# options we can fix
mdp_options_dirty = False # if set, a new mdp-file will be written
required_mdp_options = {"dihre": "yes", "dihre_fc": "1", "disre": "simple", "disre_fc": "1"}
for (k, v) in required_mdp_options.items():
if mdp_options.has_key(k):
assert mdp_options[k] == v # check, if we would overwrite something
else:
mdp_options[k] = v
mdp_options_dirty = True
if mdp_options.has_key("energygrps"):
assert "MOI" in [
str(egrp) for egrp in re.findall("[\S]+", mdp_options["energygrps"])
], "group MOI should be among energygrps in mdp file"
else:
mdp_options["energygrps"] = "MOI"
mdp_options_dirty = True
a, b = mdp_options.has_key("nstxout"), mdp_options.has_key("nstenergy")
if a and not b:
mdp_options["nstenergy"] = mdp_options["nstxout"]
mdp_options_dirty = True
elif b and not a:
mdp_options["nstxout"] = mdp_options["nstenergy"]
mdp_options_dirty = True
elif b and a:
assert mdp_options["nstxout"] == mdp_options["nstenergy"], "nstxout should equal nstenergy"
if int(mdp_options["nsteps"]) > 1e6:
msg = "Number of MD-steps?"
mdp_options["nsteps"] = str(userinput(msg, "int", default=int(mdp_options["nsteps"])))
# create a fixed mdp-file
if mdp_options_dirty:
print("Creating copy of mdp-file and adding missing options.")
out_fn = options.grompp.rsplit(".", 1)[0] + "_fixed.mdp"
f = open(out_fn, "w") # append
f.write("; Generated by zgf_create_pool\n")
for i in mdp_options.items():
f.write("%s = %s\n" % i)
f.write("; EOF\n")
f.close()
options.grompp = out_fn
# check if subsampling is reasonable
if os.path.getsize(options.presampling) > 100e6: # 100MB
print("Presampling trajectory is large")
trr = TrrFile(options.presampling)
dt = trr.first_frame.next().t - trr.first_frame.t
trr.close()
print("Presampling timestep is %.2f ps" % dt)
if dt < 10: # picoseconds
# TODO: maybe calculate subsampling factor individually, or ask?
msg = "Subsample presampling trajectory by a tenth?"
if userinput(msg, "bool"):
out_fn = options.presampling.rsplit(".", 1)[0] + "_tenth.trr"
cmd = ["trjconv", "-f", options.presampling, "-o", out_fn, "-skip", "10"]
check_call(cmd)
options.presampling = out_fn
# balance linears
if options.balance_linears:
print("Balance Linears")
old_converter = Converter(options.internals)
print("Loading presampling....")
frames = old_converter.read_trajectory(options.presampling)
new_coord_list = []
for c in old_converter:
if not isinstance(c, LinearCoordinate):
new_coord_list.append(c)
continue # we do not work on other Coordinate-Types
# TODO: is this a good way to determine new_weight and new_offset???
new_weight = c.weight / sqrt(2 * frames.var().getcoord(c))
new_offset = c.offset + frames.mean().getcoord(c)
new_coord = LinearCoordinate(*c.atoms, label=c.label, weight=new_weight, offset=new_offset)
new_coord_list.append(new_coord)
new_converter = Converter(coord_list=new_coord_list)
assert old_converter.filename.endswith(".int")
options.internals = old_converter.filename[:-4] + "_balanced.int"
print("Writing balanced Converter to: " + options.internals)
f = open(options.internals, "w")
f.write(new_converter.serialize())
f.close()
assert len(Converter(options.internals)) == len(new_coord_list) # try parsing
# Finally: Create root-node and pool
pool = Pool()
if len(pool) != 0:
print("ERROR: A pool already exists here.")
sys.exit(1)
pool.int_fn = options.internals
pool.mdp_fn = options.grompp
pool.top_fn = options.topology
pool.ndx_fn = options.index
pool.temperature = options.temperature
pool.gr_threshold = options.gr_threshold
pool.gr_chains = options.gr_chains
pool.alpha = None
pool.save() # save pool for the first time...
# ... then we can save the first node...
node0 = Node()
node0.state = "refined"
node0.save() # also creates the node directory ... needed for symlink
os.symlink(os.path.relpath(options.presampling, node0.dir), node0.trr_fn)
os.symlink(os.path.relpath(options.molecule, node0.dir), node0.pdb_fn)
pool.root_name = node0.name
pool.save() # ... now we have to save the pool again.
if not path.exists("analysis"):
os.mkdir("analysis")
def main():
options = options_desc.parse_args(sys.argv)[0]
if(options.common_filename):
options.molecule = options.common_filename+".pdb"
options.presampling = options.common_filename+".trr"
options.internals = options.common_filename+".int"
options.grompp = options.common_filename+".mdp"
options.topology = options.common_filename+".top"
options.index = options.common_filename+".ndx"
print("Options:\n%s\n"%pformat(eval(str(options))))
assert(path.exists(options.molecule))
assert(path.exists(options.presampling))
assert(path.exists(options.internals))
assert(path.exists(options.grompp))
assert(path.exists(options.topology))
#TODO: what if there is no index-file? (make_ndx)
assert(path.exists(options.index))
assert('moi' in gromacs.read_index_file(options.index)), "group 'MOI' should be defined in index file"
# checks e.g. if the mdp-file looks good
mdp_options = gromacs.read_mdp_file(options.grompp)
temperatures = [ref_t for ref_t in re.findall("[0-9]+", mdp_options["ref_t"])]
assert(len(set(temperatures)) == 1), "temperature definition in mdp file is ambiguous"
temperature = temperatures[0]
# get sampling temperature from mdp file
if(int(temperature) > 310):
if not(userinput("Your sampling temperature is set to %s K. Continue?"%temperature, "bool")):
sys.exit("Quit by user.")
# options we can fix
mdp_options_dirty = False #if set, a new mdp-file will be written
# the value of the following options need to be fixed
critical_mdp_options = {"dihre":"yes", "dihre_fc":"1", "disre":"simple", "disre_fc":"1", "gen_temp":temperature}
for (k,v) in critical_mdp_options.items():
if(mdp_options.has_key(k) and mdp_options[k].strip() != v):
print "Error. I do not want to use '%s' for option '%s' ('%s' required). Please fix your mdp file."%(mdp_options[k].strip(),k,v)
sys.exit("Quitting.")
else:
mdp_options[k] = v
mdp_options_dirty = True
# the value of the following options does not matter, but they should be there
noncritical_mdp_options = {"tcoupl":"no", "pcoupl":"no", "gen_vel":"no", "gen_seed":"-1"}
for (k,v) in noncritical_mdp_options.items():
if not(mdp_options.has_key(k)):
mdp_options[k] = v
mdp_options_dirty = True
a = mdp_options.has_key("energygrps") and "moi" not in [str(egrp) for egrp in re.findall('[\S]+', mdp_options["energygrps"])]
b = not(mdp_options.has_key("energygrps"))
if(a or b):
if not(userinput("'MOI' is not defined as an energy group in your mdp file. Maybe you have forgotten to define proper 'energygrps'. Continue?", "bool")):
sys.exit("Quit by user.")
a, b = mdp_options.has_key("nstxout"), mdp_options.has_key("nstenergy")
if(a and not b):
mdp_options["nstenergy"] = mdp_options["nstxout"]
mdp_options_dirty = True
elif(b and not a):
mdp_options["nstxout"] = mdp_options["nstenergy"]
mdp_options_dirty = True
elif(b and a):
assert(mdp_options["nstxout"] == mdp_options["nstenergy"]), "nstxout should equal nstenergy"
if(int(mdp_options["nsteps"]) > 1e6):
msg = "Number of MD-steps?"
mdp_options["nsteps"] = str( userinput(msg, "int", default=int(mdp_options["nsteps"])) )
# create a fixed mdp-file
if(mdp_options_dirty):
print("Creating copy of mdp-file and adding missing options.")
out_fn = options.grompp.rsplit(".", 1)[0] + "_fixed.mdp"
f = open(out_fn, "w") # append
f.write("; Generated by zgf_create_pool\n")
for i in sorted(mdp_options.items()):
f.write("%s = %s\n"%i)
f.write("; EOF\n")
f.close()
options.grompp = out_fn
# check if subsampling is reasonable
if(os.path.getsize(options.presampling) > 100e6): # 100MB
print("Presampling trajectory is large")
trr = TrrFile(options.presampling)
dt = trr.first_frame.next().t - trr.first_frame.t
trr.close()
print("Presampling timestep is %.2f ps"%dt)
if(dt < 10): # picoseconds
#TODO: maybe calculate subsampling factor individually, or ask?
msg = "Subsample presampling trajectory by a tenth?"
if(userinput(msg, "bool")):
out_fn = options.presampling.rsplit(".", 1)[0] + "_tenth.trr"
cmd = ["trjconv", "-f", options.presampling, "-o", out_fn, "-skip", "10"]
check_call(cmd)
options.presampling = out_fn
# balance linears
if(options.balance_linears):
print("Balance Linears")
old_converter = Converter(options.internals)
print("Loading presampling....")
frames = old_converter.read_trajectory(options.presampling)
new_coord_list = []
for c in old_converter:
if(not isinstance(c, LinearCoordinate)):
new_coord_list.append(c)
continue # we do not work on other Coordinate-Types
#TODO: is this a good way to determine new_weight and new_offset???
new_weight = c.weight / sqrt(2*frames.var().getcoord(c))
new_offset = c.offset + frames.mean().getcoord(c)
new_coord = LinearCoordinate(*c.atoms, label=c.label, weight=new_weight, offset=new_offset)
new_coord_list.append(new_coord)
new_converter = Converter(coord_list=new_coord_list)
assert(old_converter.filename.endswith(".int"))
options.internals = old_converter.filename[:-4] + "_balanced.int"
print("Writing balanced Converter to: "+options.internals)
f = open(options.internals, "w")
f.write(new_converter.serialize())
f.close()
assert(len(Converter(options.internals)) == len(new_coord_list)) #try parsing
# Finally: Create root-node and pool
pool = Pool()
if(len(pool) != 0):
print("ERROR: A pool already exists here.")
sys.exit(1)
pool.int_fn = options.internals
pool.mdp_fn = options.grompp
pool.top_fn = options.topology
pool.ndx_fn = options.index
pool.temperature = int(temperature)
pool.gr_threshold = options.gr_threshold
pool.gr_chains = options.gr_chains
pool.alpha = None
pool.save() # save pool for the first time...
# ... then we can save the first node...
node0 = Node()
node0.state = "refined"
node0.save() # also creates the node directory ... needed for symlink
os.symlink(os.path.relpath(options.presampling, node0.dir), node0.trr_fn)
os.symlink(os.path.relpath(options.molecule, node0.dir), node0.pdb_fn)
pool.root_name = node0.name
pool.save() #... now we have to save the pool again.
if(not path.exists("analysis")):
os.mkdir("analysis")
def process(node, options):
if(node.extensions_counter > 0):
cmd0 = ["tpbconv", "-s", node.tpr_fn, "-o", node.tpr_fn, "-extend", str(node.extensions_length)]
print("Calling: %s"%" ".join(cmd0))
check_call(cmd0)
cmd1 = ["mdrun"]
cmd1 += ["-s", "../../"+node.tpr_fn]
if(node.state == "em-mdrun-able"):
cmd1 += ["-c", "../../"+node.pdb_fn]
cmd1 += ["-o", "../../"+node.dir+"/em.trr"]
cmd1 += ["-e", "../../"+node.dir+"/em.edr"]
cmd1 += ["-g", "../../"+node.dir+"/em.log"]
else:
cmd1 += ["-o", "../../"+node.trr_fn]
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"]
# use mpiexec and mdrun_mpi if available
if(not options.seq and call(["which","mpiexec"])==0):
if(call(["which","mdrun_mpi"])==0):
cmd1[0] = "mdrun_mpi"
cmd1 = ["mpiexec", "-np", 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
# check for convergence
converged = conv_check_gelman_rubin(node)
# decide what to do next
if(converged):
node.state = "converged"
elif(node.extensions_counter >= node.extensions_max):
node.state = "not-converged"
else:
node.extensions_counter += 1
node.state = "mdrun-able" # actually it should still be in this state
def main():
options = options_desc.parse_args(sys.argv)[0]
if (options.common_filename):
options.molecule = options.common_filename + ".pdb"
options.presampling = options.common_filename + ".trr"
options.internals = options.common_filename + ".int"
options.grompp = options.common_filename + ".mdp"
options.topology = options.common_filename + ".top"
options.index = options.common_filename + ".ndx"
print("Options:\n%s\n" % pformat(eval(str(options))))
assert (path.exists(options.molecule))
assert (path.exists(options.presampling))
assert (path.exists(options.internals))
assert (path.exists(options.grompp))
assert (path.exists(options.topology))
#TODO: what if there is no index-file? (make_ndx)
assert (path.exists(options.index))
assert ('moi' in gromacs.read_index_file(
options.index)), "group 'MOI' should be defined in index file"
# checks e.g. if the mdp-file looks good
mdp_options = gromacs.read_mdp_file(options.grompp)
temperatures = [
ref_t for ref_t in re.findall("[0-9]+", mdp_options["ref_t"])
]
assert (len(set(temperatures)) == 1
), "temperature definition in mdp file is ambiguous"
temperature = temperatures[0]
# get sampling temperature from mdp file
if (int(temperature) > 310):
if not (userinput(
"Your sampling temperature is set to %s K. Continue?" %
temperature, "bool")):
sys.exit("Quit by user.")
# options we can fix
mdp_options_dirty = False #if set, a new mdp-file will be written
# the value of the following options need to be fixed
critical_mdp_options = {
"dihre": "yes",
"dihre_fc": "1",
"disre": "simple",
"disre_fc": "1",
"gen_temp": temperature
}
for (k, v) in critical_mdp_options.items():
if (mdp_options.has_key(k) and mdp_options[k].strip() != v):
print "Error. I do not want to use '%s' for option '%s' ('%s' required). Please fix your mdp file." % (
mdp_options[k].strip(), k, v)
sys.exit("Quitting.")
else:
mdp_options[k] = v
mdp_options_dirty = True
# the value of the following options does not matter, but they should be there
noncritical_mdp_options = {
"tcoupl": "no",
"pcoupl": "no",
"gen_vel": "no",
"gen_seed": "-1"
}
for (k, v) in noncritical_mdp_options.items():
if not (mdp_options.has_key(k)):
mdp_options[k] = v
mdp_options_dirty = True
a = mdp_options.has_key("energygrps") and "moi" not in [
str(egrp) for egrp in re.findall('[\S]+', mdp_options["energygrps"])
]
b = not (mdp_options.has_key("energygrps"))
if (a or b):
if not (userinput(
"'MOI' is not defined as an energy group in your mdp file. Maybe you have forgotten to define proper 'energygrps'. Continue?",
"bool")):
sys.exit("Quit by user.")
a, b = mdp_options.has_key("nstxout"), mdp_options.has_key("nstenergy")
if (a and not b):
mdp_options["nstenergy"] = mdp_options["nstxout"]
mdp_options_dirty = True
elif (b and not a):
mdp_options["nstxout"] = mdp_options["nstenergy"]
mdp_options_dirty = True
elif (b and a):
assert (mdp_options["nstxout"] == mdp_options["nstenergy"]
), "nstxout should equal nstenergy"
if (int(mdp_options["nsteps"]) > 1e6):
msg = "Number of MD-steps?"
mdp_options["nsteps"] = str(
userinput(msg, "int", default=int(mdp_options["nsteps"])))
# create a fixed mdp-file
if (mdp_options_dirty):
print("Creating copy of mdp-file and adding missing options.")
out_fn = options.grompp.rsplit(".", 1)[0] + "_fixed.mdp"
f = open(out_fn, "w") # append
f.write("; Generated by zgf_create_pool\n")
for i in sorted(mdp_options.items()):
f.write("%s = %s\n" % i)
f.write("; EOF\n")
f.close()
options.grompp = out_fn
# check if subsampling is reasonable
if (os.path.getsize(options.presampling) > 100e6): # 100MB
print("Presampling trajectory is large")
trr = TrrFile(options.presampling)
dt = trr.first_frame.next().t - trr.first_frame.t
trr.close()
print("Presampling timestep is %.2f ps" % dt)
if (dt < 10): # picoseconds
#TODO: maybe calculate subsampling factor individually, or ask?
msg = "Subsample presampling trajectory by a tenth?"
if (userinput(msg, "bool")):
out_fn = options.presampling.rsplit(".", 1)[0] + "_tenth.trr"
cmd = [
"trjconv", "-f", options.presampling, "-o", out_fn,
"-skip", "10"
]
check_call(cmd)
options.presampling = out_fn
# balance linears
if (options.balance_linears):
print("Balance Linears")
old_converter = Converter(options.internals)
print("Loading presampling....")
frames = old_converter.read_trajectory(options.presampling)
new_coord_list = []
for c in old_converter:
if (not isinstance(c, LinearCoordinate)):
new_coord_list.append(c)
continue # we do not work on other Coordinate-Types
#TODO: is this a good way to determine new_weight and new_offset???
new_weight = c.weight / sqrt(2 * frames.var().getcoord(c))
new_offset = c.offset + frames.mean().getcoord(c)
new_coord = LinearCoordinate(*c.atoms,
label=c.label,
weight=new_weight,
offset=new_offset)
new_coord_list.append(new_coord)
new_converter = Converter(coord_list=new_coord_list)
assert (old_converter.filename.endswith(".int"))
options.internals = old_converter.filename[:-4] + "_balanced.int"
print("Writing balanced Converter to: " + options.internals)
f = open(options.internals, "w")
f.write(new_converter.serialize())
f.close()
assert (len(Converter(options.internals)) == len(new_coord_list)
) #try parsing
# Finally: Create root-node and pool
pool = Pool()
if (len(pool) != 0):
print("ERROR: A pool already exists here.")
sys.exit(1)
pool.int_fn = options.internals
pool.mdp_fn = options.grompp
pool.top_fn = options.topology
pool.ndx_fn = options.index
pool.temperature = int(temperature)
pool.gr_threshold = options.gr_threshold
pool.gr_chains = options.gr_chains
pool.alpha = None
pool.save() # save pool for the first time...
# ... then we can save the first node...
node0 = Node()
node0.state = "refined"
node0.save() # also creates the node directory ... needed for symlink
os.symlink(os.path.relpath(options.presampling, node0.dir), node0.trr_fn)
os.symlink(os.path.relpath(options.molecule, node0.dir), node0.pdb_fn)
pool.root_name = node0.name
pool.save() #... now we have to save the pool again.
if (not path.exists("analysis")):
os.mkdir("analysis")
def main():
options = options_desc.parse_args(sys.argv)[0]
pool = Pool()
needy_nodes = pool.where("state == 'merge-able'").multilock()
if (len(needy_nodes) == 0):
return
# find out about trr time step
dt = 0
nodeDir = needy_nodes[0].dir.split('/')[-1]
for fn in os.listdir(needy_nodes[0].dir):
if re.match("^" + nodeDir + ".+run\d+\.trr", fn):
trr = TrrFile(needy_nodes[0].dir + "/" + fn)
dt = trr.first_frame.next().t - trr.first_frame.t
trr.close()
break
# dt is sometimes noisy in the final digits (three digits is femtosecond step = enough)
dt = np.around(dt, decimals=3)
for n in needy_nodes:
if (options.trr):
# merge sampling trajectories
trr_fns = sorted([
fn for fn in os.listdir(n.dir)
if re.match("[^#].+run\d+.trr", fn)
])
cmd = ["trjcat", "-f"]
cmd += trr_fns
cmd += ["-o", "../../" + n.trr_fn, "-cat"]
print("Calling: %s" % " ".join(cmd))
check_call(cmd, cwd=n.dir)
if (options.edr):
# merge edr files
# get list of edr-files
edr_fnames = sorted([
n.dir + "/" + fn for fn in os.listdir(n.dir)
if re.match("[^#].+run\d+.edr", fn)
])
assert (len(edr_fnames) == n.extensions_counter + 1)
assert (len(edr_fnames) == n.extensions_max + 1)
time_offset = n.sampling_length + dt
for edr_fn in edr_fnames[1:]:
# adapt edr starting times
cmd = ["eneconv", "-f", edr_fn, "-o", edr_fn, "-settime"]
print("Calling: " + (" ".join(cmd)))
p = Popen(cmd, stdin=PIPE)
p.communicate(input=(str(time_offset) + "\n"))
assert (p.wait() == 0)
time_offset += n.extensions_length + dt
# concatenate edr files with adapted starting times
cmd = ["eneconv", "-f"] + edr_fnames + ["-o", n.dir + "/ener.edr"]
print("Calling: " + (" ".join(cmd)))
p = Popen(cmd)
retcode = p.wait()
assert (retcode == 0)
needy_nodes.unlock()