def make_res_x(iter_index, json_file):
fp = open(json_file, 'r')
jdata = json.load(fp)
nsteps = jdata["res_nsteps"]
gmx_prep = jdata["gmx_prep"]
gmx_run = jdata["gmx_run"]
frame_freq = jdata["res_frame_freq"]
base_path = os.getcwd() + "/"
string_path = base_path + libr.make_iter_name(iter_index) + "/"
string_equi_path = base_path + libr.make_iter_name(iter_index - 1) + "/"
res_path = string_path + res_name + "/"
if iter_index == 0:
res_equi_path = string_path + res_name + ".equi" + "/"
else:
res_equi_path = string_equi_path + res_name + "/"
templ_mol_path = template_path + "/" + mol_name + "/"
templ_res_path = template_path + "/" + res_name + "/"
libr.create_path(res_path)
string = np.loadtxt(string_path + "string.out")
numb_node = string.shape[0]
task_dirs = []
task_args = []
for ii in range(0, numb_node):
node_name = "%06d" % ii
work_path = res_path + node_name + "/"
equi_path = res_equi_path + node_name + "/"
libr.create_path(work_path)
libr.copy_file_list(res_files, templ_res_path, work_path)
libr.copy_file_list(mol_files, templ_mol_path, work_path)
os.symlink(equi_path + "confout.gro", work_path + "conf.gro")
## simul
arg_str = libr.list_to_arg(string[ii])
# libr.log_task ("./mkres.sh " + arg_str)
# sp.check_call("./mkres.sh " + arg_str, shell = True)
task_dirs.append(work_path)
task_args.append(arg_str)
global exec_machine
libr.exec_hosts(exec_machine, "./mkres.sh", 1, task_dirs, task_args)
for ii in range(0, numb_node):
node_name = "%06d" % ii
work_path = res_path + node_name + "/"
os.chdir(work_path)
libr.make_grompp_res("grompp.mdp", nsteps, frame_freq)
libr.replace(work_path + res_plm, "STRIDE=[^ ]* ",
"STRIDE=%d " % frame_freq)
os.chdir(base_path)
def run_res(iter_index, json_file, res_name_suffix=""):
fp = open(json_file, 'r')
jdata = json.load(fp)
gmx_prep = jdata["gmx_prep"]
gmx_run = jdata["gmx_run"]
res_thread = jdata["res_thread"]
gmx_run = gmx_run + (" -nt %d " % res_thread)
gmx_run = gmx_run + " -plumed " + res_plm
gmx_prep_log = "gmx_grompp.log"
gmx_run_log = "gmx_mdrun.log"
gmx_prep_cmd = libr.cmd_append_log(gmx_prep, gmx_prep_log)
gmx_run_cmd = libr.cmd_append_log(gmx_run, gmx_run_log)
iter_name = libr.make_iter_name(iter_index)
res_path = iter_name + "/" + res_name + res_name_suffix + "/"
base_path = os.getcwd() + "/"
if not os.path.isdir(res_path):
raise RuntimeError("do not see any restrained simulation (%s)." %
res_path)
all_task = glob.glob(res_path + "/[0-9]*[0-9]")
all_task.sort()
# run_node_tasks(max_thread, 1, all_task, gmx_prep_cmd)
# run_node_tasks(max_thread, res_thread, all_task, gmx_run_cmd)
global exec_machine
libr.exec_hosts(exec_machine, gmx_prep_cmd, 1, all_task, None)
libr.exec_hosts(exec_machine, gmx_run_cmd, res_thread, all_task, None)
def make_string(iter_index, string):
iter_name = libr.make_iter_name(iter_index)
base_path = os.getcwd() + "/"
string_path = base_path + iter_name + "/"
libr.create_path(string_path)
os.chdir(string_path)
np.savetxt("string.out", string)
os.chdir(base_path)
def compute_force(iter_index, string_):
base_path = os.getcwd() + "/"
iter_name = libr.make_iter_name(iter_index)
string_path = base_path + iter_name + "/"
string = np.loadtxt(string_path + "string.out")
norm_diff = np.linalg.norm(string_ - string)
if (norm_diff > 1e-5):
raise RuntimeError("inconsistent string")
return np.loadtxt(string_path + "force.out")
def equi_old_string_parallel(json_file):
fp = open(json_file, 'r')
jdata = json.load(fp)
equi_nsteps = jdata["res_equi_nsteps"]
equi_dt = jdata["res_equi_dt"]
old_string_path = jdata["old_string_path"]
assert os.path.isdir(old_string_path)
iter_index = 0
frame_freq = 0
old_string_path = os.path.abspath(old_string_path) + "/"
base_path = os.getcwd() + "/"
iter_name = libr.make_iter_name(iter_index)
new_string_path = base_path + iter_name + "/"
res_path = new_string_path + res_name + ".equi" + "/"
templ_mol_path = template_path + "/" + mol_name + "/"
templ_res_path = template_path + "/" + res_name + "/"
old_string = np.loadtxt(old_string_path + "string.out")
new_string = np.loadtxt(new_string_path + "string.out")
old_numb_nodes = old_string.shape[0]
new_numb_nodes = new_string.shape[0]
for ii in range(new_numb_nodes):
# create working dir
node_name = "%06d" % ii
work_path = res_path + node_name + "/"
libr.create_path(work_path)
libr.copy_file_list(res_files, templ_res_path, work_path)
libr.copy_file_list(string_equi_conf_files, templ_mol_path, work_path)
# find the minimal dist old node
min_indx = 0
min_dist = np.linalg.norm(new_string[ii] - old_string[min_indx])
for jj in range(1, old_numb_nodes):
dist = np.linalg.norm(new_string[ii] - old_string[jj])
if dist < min_dist:
min_indx = jj
min_dist = dist
init_node_path = old_string_path + res_name + "/" + ("%06d" %
min_indx) + "/"
# link confs
os.symlink(init_node_path + "/confout.gro", work_path + "/conf.gro")
# setup working dir
os.chdir(work_path)
arg_str = libr.list_to_arg(new_string[ii])
libr.log_task("./mkres.sh " + arg_str)
sp.check_call("./mkres.sh " + arg_str, shell=True)
libr.make_grompp_res_equi("grompp.mdp", equi_nsteps, frame_freq,
equi_dt)
libr.replace(work_path + res_plm, "STRIDE=[^ ]* ",
"STRIDE=%d " % frame_freq)
os.chdir(base_path)
run_res(0, json_file, ".equi")
def post_res(iter_index, json_file):
fp = open(json_file, 'r')
jdata = json.load(fp)
res_cmpf_error = jdata["res_cmpf_error"]
iter_name = libr.make_iter_name(iter_index)
res_path = iter_name + "/" + res_name + "/"
base_path = os.getcwd() + "/"
string_path = base_path + iter_name + "/"
if not os.path.isdir(res_path):
raise RuntimeError("do not see any restrained simulation (%s)." %
res_path)
all_task = glob.glob(res_path + "/[0-9]*[0-9]")
all_task.sort()
if res_cmpf_error:
cmpf_cmd = "./cmpf.sh"
else:
cmpf_cmd = "./cmpf.py"
cmpf_log = "cmpf.log"
cmpf_cmd = libr.cmd_append_log(cmpf_cmd, cmpf_log)
global exec_machine
libr.exec_hosts(exec_machine, cmpf_cmd, 1, all_task, None)
centers = []
force = []
ndim = 0
for work_path in all_task:
os.chdir(work_path)
this_centers = np.loadtxt('centers.out')
centers = np.append(centers, this_centers)
this_force = np.loadtxt('force.out')
force = np.append(force, this_force)
ndim = this_force.size
assert (ndim == this_centers.size
), "center size is diff to force size in " + work_path
os.chdir(base_path)
centers = np.reshape(centers, [-1, ndim])
force = np.reshape(force, [-1, ndim])
data = np.concatenate((centers, force), axis=1)
np.savetxt(res_path + 'data.raw', data, fmt="%.6e")
# added this one...
np.savetxt(string_path + 'force.out', force, fmt="%.6e")
norm_force = np.linalg.norm(force, axis=1)
libr.log_task(
"min|f| = %e max|f| = %e avg|f| = %e" %
(np.min(norm_force), np.max(norm_force), np.average(norm_force)))
def update_string(iter_index, json_file):
fp = open(json_file, 'r')
jdata = json.load(fp)
dt = jdata["str_dt"]
weighting = [[0, 1], [1, 1]]
key = "string_weight"
if key in jdata.keys():
weighting = jdata[key]
base_path = os.getcwd() + "/"
iter_name = libr.make_iter_name(iter_index)
string_path = base_path + iter_name + "/"
string = np.loadtxt(string_path + "string.out")
numb_node = string.shape[0]
old_string = libs.resample_string(string, numb_node, weighting)
new_string = libs.update_string_Euler(compute_force, dt, iter_index,
string)
new_string = libs.resample_string(new_string, numb_node, weighting)
make_string(iter_index + 1, new_string)
return np.linalg.norm(old_string - new_string)
def equi_0_serial(json_file):
fp = open(json_file, 'r')
jdata = json.load(fp)
equi_nsteps = jdata["res_equi_nsteps"]
equi_dt = jdata["res_equi_dt"]
init_start_conf = jdata["init_start_conf"]
start_conf_name = os.path.basename(init_start_conf)
gmx_prep = jdata["gmx_prep"]
gmx_run = jdata["gmx_run"]
iter_index = 0
frame_freq = 0
gmx_prep_log = "gmx_grompp.log"
gmx_run_log = "gmx_mdrun.log"
base_path = os.getcwd() + "/"
iter_name = libr.make_iter_name(iter_index)
string_path = base_path + iter_name + "/"
res_path = string_path + res_name + ".equi" + "/"
templ_mol_path = template_path + "/" + mol_name + "/"
templ_res_path = template_path + "/" + res_name + "/"
libr.create_path(res_path)
string = np.loadtxt(string_path + "string.out")
numb_node = string.shape[0]
# case of node 0
node_name = "%06d" % 0
work_path = res_path + node_name + "/"
libr.create_path(work_path)
libr.copy_file_list(res_files, templ_res_path, work_path)
libr.copy_file_list(string_equi_conf_files, templ_mol_path, work_path)
libr.copy_file_list([init_start_conf], base_path, work_path)
os.chdir(work_path)
if not os.path.isfile("conf.gro"):
os.symlink(start_conf_name, "conf.gro")
os.chdir(base_path)
## equi simul
os.chdir(work_path)
arg_str = libr.list_to_arg(string[0])
sp.check_call("./mkres.sh " + arg_str, shell=True)
libr.log_task("./mkres.sh " + arg_str)
libr.make_grompp_res_equi("grompp.mdp", equi_nsteps, frame_freq, equi_dt)
libr.replace(work_path + res_plm, "STRIDE=[^ ]* ",
"STRIDE=%d " % frame_freq)
gmx_prep_cmd = gmx_prep
gmx_run_cmd = gmx_run + " -nt 1 " + " -plumed " + res_plm
gmx_prep_cmd = libr.cmd_append_log(gmx_prep_cmd, gmx_prep_log)
gmx_run_cmd = libr.cmd_append_log(gmx_run_cmd, gmx_prep_log)
libr.log_task(gmx_prep_cmd)
sp.check_call(gmx_prep_cmd, shell=True)
libr.log_task(gmx_run_cmd)
sp.check_call(gmx_run_cmd, shell=True)
os.chdir(base_path)
for ii in range(1, numb_node):
prev_node_name = "%06d" % (ii - 1)
node_name = "%06d" % ii
work_path = res_path + node_name + "/"
libr.create_path(work_path)
libr.copy_file_list(res_files, templ_res_path, work_path)
libr.copy_file_list(string_equi_conf_files, templ_mol_path, work_path)
os.symlink(work_path + "../" + prev_node_name + "/confout.gro",
work_path + "/conf.gro")
## equi simul
os.chdir(work_path)
arg_str = libr.list_to_arg(string[ii])
libr.log_task("./mkres.sh " + arg_str)
sp.check_call("./mkres.sh " + arg_str, shell=True)
libr.make_grompp_res_equi("grompp.mdp", equi_nsteps, frame_freq,
equi_dt)
libr.replace(work_path + res_plm, "STRIDE=[^ ]* ",
"STRIDE=%d " % frame_freq)
gmx_prep_cmd = gmx_prep
gmx_run_cmd = gmx_run + " -nt 1 " + " -plumed " + res_plm
gmx_prep_cmd = libr.cmd_append_log(gmx_prep_cmd, gmx_prep_log)
gmx_run_cmd = libr.cmd_append_log(gmx_run_cmd, gmx_prep_log)
libr.log_task(gmx_prep_cmd)
sp.check_call(gmx_prep_cmd, shell=True)
libr.log_task(gmx_run_cmd)
sp.check_call(gmx_run_cmd, shell=True)
os.chdir(base_path)