def main () :
parser = argparse.ArgumentParser(
description="*** Compute the free energy along a string. ***")
parser.add_argument('-s', '--string-folder',
help='The folder of the string to be computed.')
parser.add_argument('-o', '--output', default = "energy.out",
help='The output energy in string folder.')
args = parser.parse_args()
string_file = args.string_folder + "/string.out"
string_force = args.string_folder + "/force.out"
if not os.path.exists (string_file) :
raise RuntimeError ("cannot find string file " + string_file)
if not os.path.exists (string_force) :
raise RuntimeError ("cannot find string force file " +
string_force +
". maybe the simulation is not finished")
string = np.loadtxt (string_file)
force = np.loadtxt (string_force)
numb_node = string.shape[0]
dim = string.shape[1]
# compute arc (alpha)
alpha_seg = StringUtils.arc_seg (string)
alpha = StringUtils.arc_norm (string)
# integrate the energy
energy = np.zeros (alpha.shape)
tagent = compute_string_tegent (alpha, string)
for ii in range (1, numb_node) :
v0 = np.dot (tagent[ii-1], force[ii-1])
v1 = np.dot (tagent[ii] , force[ii] )
vn = force[ii] - v1 * tagent[ii]
# print (str(v1) +
# " t: " + str(v1 * tagent[ii]) +
# " |t|: " + str(np.sqrt(np.dot(v1 * tagent[ii], v1 * tagent[ii]))) +
# " n: " + str(vn) +
# " |n|: " + str(np.sqrt(np.dot(vn,vn))) +
# " t.n: " + str(np.dot(v1 * tagent[ii], vn))
# )
de = 0.5 * (v0 + v1) * alpha_seg[ii]
energy[ii] = energy[ii-1] - de
new_shape = np.array ([alpha.shape[0], 2])
result = np.zeros (new_shape)
result[:,0] = alpha
result[:,1] = energy
string_energy = args.string_folder + "/energy.out"
np.savetxt (string_energy, result)
def init_source_string (string_dir, numb_node_tgt) :
""" init a string from existing nodes"""
if not os.path.isdir (string_dir) :
raise RuntimeError ("Dir " + string_dir + " not found")
file_name = string_dir + "/string.out"
if not os.path.exists (file_name) :
raise RuntimeError ("cannot find file " + file_name)
string = np.loadtxt (file_name)
alpha = StringUtils.arc_norm (string)
smooth_str = interp1d (alpha, string, axis=0, kind="linear")
alpha_eq = np.linspace (0, 1, numb_node_tgt)
string = smooth_str (alpha_eq)
return string
def init_source_string(string_dir, numb_node_tgt):
""" init a string from existing nodes"""
if not os.path.isdir(string_dir):
raise RuntimeError("Dir " + string_dir + " not found")
file_name = string_dir + "/string.out"
if not os.path.exists(file_name):
raise RuntimeError("cannot find file " + file_name)
string = np.loadtxt(file_name)
alpha = StringUtils.arc_norm(string)
smooth_str = interp1d(alpha, string, axis=0, kind="linear")
alpha_eq = np.linspace(0, 1, numb_node_tgt)
string = smooth_str(alpha_eq)
return string
def generate_from_source (source_string_dir_,
string) :
# check the dir and string file
if not os.path.isdir (source_string_dir_) :
raise RuntimeError ("cannot find dir " + source_string_dir_)
cwd = os.getcwd()
os.chdir (source_string_dir_)
source_string_dir = os.getcwd ()
os.chdir (cwd)
file_name = source_string_dir + "/string.out"
if not os.path.exists (file_name) :
raise RuntimeError ("cannot find file " + file_name)
# load source string
source_string = np.loadtxt (file_name)
if source_string.shape[1] != string.shape[1] :
raise RuntimeError ("size of the string nodes does not match")
# mk dir of the string
str_force = StringForce ()
string_name = str_force.mk_string_name (0)
if not os.path.isdir(string_name) :
ret = Popen(["cp", '-a', str_force.string_template, string_name], stdout=PIPE, stderr=PIPE)
stdout, stderr = ret.communicate()
if ret.returncode != 0 :
raise RuntimeError ("cannot copy template dir to " + string_name)
# generate nodes
cwd = os.getcwd()
cmd_gen_dir = "tools/gen.dir.absdep.sh"
os.chdir (string_name)
my_alpha = StringUtils.arc_norm (string)
source_alpha = StringUtils.arc_norm (source_string)
for ii in range (string.shape[0]) :
# min_val = 1e10
# min_posi = 0
# for jj in range(source_string.shape[0]) :
# norm = np.linalg.norm (string[ii] - source_string[jj])
# # print ("id " + str(jj) +
# # " diff " + str(string[ii]) + " " + str(source_string[jj]) + " norm " + str(norm))
# if norm < min_val :
# min_val = norm
# min_posi = jj
for jj in range(source_string.shape[0]) :
if (my_alpha[ii] >= source_alpha[jj]) :
min_posi = jj
this_node = str_force.mk_node_name (ii)
str_force.mk_node_param (string[ii])
source_node = str_force.mk_node_name (min_posi)
ret = Popen ([cmd_gen_dir, this_node, source_string_dir+"/"+source_node], stdout=PIPE, stderr=PIPE)
stdout, stderr = ret.communicate()
if ret.returncode == 1 :
raise RuntimeError ("cannot generate node. LOCATION: string: " +
string_name +
" node index: " +
str(this_node) +
". error info: " +
str(stderr, encoding='ascii') )
if ret.returncode == 10 :
print ("# detected node: " + string_name + "/" + this_node)
else :
print ("# generated node: " + string_name + "/" + this_node)
np.savetxt ("string.out", string)
os.chdir (cwd)
def generate_from_source(source_string_dir_, string):
# check the dir and string file
if not os.path.isdir(source_string_dir_):
raise RuntimeError("cannot find dir " + source_string_dir_)
cwd = os.getcwd()
os.chdir(source_string_dir_)
source_string_dir = os.getcwd()
os.chdir(cwd)
file_name = source_string_dir + "/string.out"
if not os.path.exists(file_name):
raise RuntimeError("cannot find file " + file_name)
# load source string
source_string = np.loadtxt(file_name)
if source_string.shape[1] != string.shape[1]:
raise RuntimeError("size of the string nodes does not match")
# mk dir of the string
str_force = StringForce()
string_name = str_force.mk_string_name(0)
if not os.path.isdir(string_name):
ret = Popen(["cp", '-a', str_force.string_template, string_name],
stdout=PIPE,
stderr=PIPE)
stdout, stderr = ret.communicate()
if ret.returncode != 0:
raise RuntimeError("cannot copy template dir to " + string_name)
# generate nodes
cwd = os.getcwd()
cmd_gen_dir = "tools/gen.dir.absdep.sh"
os.chdir(string_name)
my_alpha = StringUtils.arc_norm(string)
source_alpha = StringUtils.arc_norm(source_string)
for ii in range(string.shape[0]):
# min_val = 1e10
# min_posi = 0
# for jj in range(source_string.shape[0]) :
# norm = np.linalg.norm (string[ii] - source_string[jj])
# # print ("id " + str(jj) +
# # " diff " + str(string[ii]) + " " + str(source_string[jj]) + " norm " + str(norm))
# if norm < min_val :
# min_val = norm
# min_posi = jj
for jj in range(source_string.shape[0]):
if (my_alpha[ii] >= source_alpha[jj]):
min_posi = jj
this_node = str_force.mk_node_name(ii)
str_force.mk_node_param(string[ii])
source_node = str_force.mk_node_name(min_posi)
ret = Popen(
[cmd_gen_dir, this_node, source_string_dir + "/" + source_node],
stdout=PIPE,
stderr=PIPE)
stdout, stderr = ret.communicate()
if ret.returncode == 1:
raise RuntimeError("cannot generate node. LOCATION: string: " +
string_name + " node index: " + str(this_node) +
". error info: " +
str(stderr, encoding='ascii'))
if ret.returncode == 10:
print("# detected node: " + string_name + "/" + this_node)
else:
print("# generated node: " + string_name + "/" + this_node)
np.savetxt("string.out", string)
os.chdir(cwd)
