def p4b_run(saves):
saves = p3_run(saves)
if "first_string" not in saves:
print("Creating VIS string object")
saves["first_string"] = vc.VIS_string(start=saves["startVIS"],
end=saves["endVIS"],
string=saves["intermed"],
no_CVs=2)
save(saves)
saves["first_string"].create_SO()
if "b_act" not in saves:
saves["b_act"] = str(saves["first_string"])
save(saves)
end_loc = saves["first_string"].run_swarms()
save(saves)
"""
print("before, intended:")
print(np.array(saves["CVstates"]))
print("before, actual:")
print(saves["b_act"])
print("\nafter:")
print(end_loc)
"""
return saves
def p4b_run():
#reuse = input("use previous run (y/n)")=="y"
reuse = True
#reuse = True
debug = True
#debug = False
if reuse:
saves = load()
p3_run(saves)
else:
saves = p3_run({})
if "first_string" not in saves:
saves["first_string"] = vc.VIS_string(start=saves["startVIS"],
end=saves["endVIS"],
string=saves["intermed"],
no_CVs=2)
save(saves)
saves["first_string"].create_SO()
if "b_act" not in saves:
saves["b_act"] = str(saves["first_string"])
save(saves)
end_loc = saves["first_string"].run_swarms()
save(saves)
print("before, intended:")
print(np.array(saves["CVstates"]))
print("before, actual:")
print(saves["b_act"])
print("\nafter:")
print(end_loc)
if debug:
all_trajs(saves)
def p4a_run():
#reuse = input("use previous run (y/n)")=="y"
reuse = False
#reuse = True
#debug = True
debug = False
if reuse:
saves = load()
p3_run(saves)
else:
saves = p3_run({})
if "one" not in saves:
saves["one"] = saves["intermed"][0]
save(saves)
if "first_swarm" not in saves or debug:
saves["first_swarm"] = vc.VIS_swarm(saves["one"])
save(saves)
saves["first_swarm"].run_swarm()
save(saves)
aver = saves["first_swarm"].averages()
aver = np.mean(aver, axis=0)
import VIS_col as VC
from md_tools import *
if __name__ == "__main__":
a = load()
if a == {}:
shutil.copyfile("topol_orig.top", "topol.top")
a = VC.VIS_collection("parameters.smg")
a.parse_parameters()
a.prepare_endpoints()
a.create_base_string()
a.run_method()