def get_strain_e(ParaIn, dstpath, StrainMode, BaseVec, strain = 0.0, Modei = 0):
StrainOrMode = "Strain"
if Modei == 0:
StrainOrMode = "Mode"
(flag_se, flag_continue, BaseName, RunStr, PreName) = getparam(ParaIn, dstpath, StrainOrMode)
#BaseVec = eglue.get_base_vec(BaseName)
Efilename = PreName + "_" + StrainOrMode + ".txt"
if flag_continue:
os.chdir(dstpath)
#E0 is energy for strain-energy method, and stress for strain-stress method
E0 = get_continue_strain_e(Efilename, flag_se, strain, Modei)
if Modei == 0:
os.chdir("../../")
else:
if Modei == 0:
esutils.creat_folder(BaseName)
shutil.copyfile("INPUT", BaseName + "/INPUT")
#print os.getcwd()
esutils.creat_folder(dstpath)
eglue.copy_files(BaseName, dstpath)
os.chdir(dstpath)
if Modei > 0:
StrainMatrix = strain*StrainMode[Modei-1]
BaseVecNew = BaseVec .dot (crydef.strain2deformgrad(StrainMatrix))
crylat.print_lattice(BaseVecNew)
eglue.write_base_vec(BaseName, BaseVecNew)
os.system(RunStr + ">> FP_OUT")
E0 = get_org_strain_e(BaseName, flag_se)
print(E0)
np.savetxt(Efilename, E0)
if Modei == 0:
os.chdir("../../")
return E0
def get_strain_e(ParaIn, dstpath, StrainMode, BaseVec, strain=0.0, Modei=0):
'''
In the strain folder, run first principles code and get the energy
Parameters
----------
ParaIn: dict
The dict of input parameters
dstpath: str
The destination path
StrainMode: 3D np.ndarray, size: nx3x3
The strain mode.
BaseVec: np.ndarray
The crystal vector
strain: float
The value of the strain. e.g. 0.03
Modei: int
The ith strain mode. When modei=0, it means the undeformed structure
Return
------
E0: list
The energy of current strain. in multi unit
'''
StrainOrMode = "Strain"
if Modei == 0:
StrainOrMode = "Mode"
(flag_se, flag_continue, BaseName, RunStr,
PreName) = getparam(ParaIn, dstpath, StrainOrMode)
EnergyCode = ParaIn['EnergyCode'].lower()
eglue = importlib.import_module('elastic3rd.energy.{}'.format(EnergyCode))
#BaseVec = eglue.get_base_vec(BaseName)
Efilename = PreName + "_" + StrainOrMode + ".txt"
if flag_continue:
os.chdir(dstpath)
#E0 is energy for strain-energy method, and stress for strain-stress method
E0 = get_continue_strain_e(Efilename, flag_se, strain, Modei)
if Modei == 0:
os.chdir("../../")
else:
if Modei == 0:
esutils.creat_folder(BaseName)
shutil.copyfile("INPUT", BaseName + "/INPUT")
#print os.getcwd()
esutils.creat_folder(dstpath)
eglue.copy_files(BaseName, dstpath)
os.chdir(dstpath)
if Modei > 0:
StrainMatrix = strain * StrainMode[Modei - 1]
BaseVecNew = BaseVec.dot(crydef.strain2deformgrad(StrainMatrix))
crylat.print_lattice(BaseVecNew)
eglue.write_base_vec(BaseName, BaseVecNew)
os.system(RunStr + ">> FP_OUT")
E0 = get_org_strain_e(BaseName, flag_se, EnergyCode=EnergyCode)
np.savetxt(Efilename, E0)
if Modei == 0:
os.chdir("../../")
return E0
def elastic3(INPUT = "INPUT"):
#Print LOGO
esutils.print_logo()
#Read INPUT
#ParaIn = esutils.read_input(INPUT)
print("===================The input parameters===================")
esutils.print_parain(ParaIn)
flag_se = ParaIn['FlagSE'].lower()
#Import glue as eglue
#eglue = __import__("energy." + ParaIn['EnergyCode'], fromlist = ParaIn['EnergyCode'])
#Deform mode this is for cubic
#TODO : for any symmtry
CrystalType = ParaIn['CrystalType']
Ord = ParaIn['Ord']
CalMode = ParaIn['CalMode'].lower()
#StrainMode = []
if CalMode == 's':
StrainIn = esutils.read_strainmode()
if flag_se == "e":
Cij_mode, coef_e, StrainMode = essym.CoefForSingleMode(CrystalType, Ord, StrainIn)
elif flag_se == "s":
pass
elif CalMode == 'w':
if flag_se == "e":
coef_e, StrainMode = essym.gen_strain_mode(CrystalType, Ord)
elif flag_se == "s":
pass
#Mode_index = range(1, 7)
StrainList = esutils.gen_strain_list(ParaIn)
n_Strain = len(StrainList)
n_Mode = StrainMode.shape[0]
#n_Mode = len(Mode_index)
E = np.zeros((n_Strain, n_Mode))
if flag_se == "s":
E = np.zeros((n_Strain, 6*n_Mode))
if flag_se == "e":
Efilename_Mode = "Energy_Mode.txt"
elif flag_se == "s":
Efilename_Mode = "Stress_Mode.txt"
#Get the energy run string
BaseName = ParaIn['BaseName']
if ParaIn['EnergyRun']:
RunStr = eglue.run(ParaIn['NP'], BaseName)
else:
RunStr = energy.glue.run()
#os.system(RunStr)
#Get the base vector
BaseVec = eglue.get_base_vec(BaseName)
print("====================Crystal Structure====================")
V0 = crylat.print_lattice(BaseVec)
#Calculate the energy of undeformed structure
# creat the folder Mode0
dstpath = BaseName + "/Mode0"
E0 = get_strain_e(ParaIn, dstpath, StrainMode, BaseVec)
if CalMode == 's':
shutil.copyfile("STRAINMODE", BaseName + "/STRAINMODE")
#print("\n")
print("\n==================Deformed Crystal========================")
#print E
for i in range(1, n_Mode + 1):
print("----------------------------------------------------------")
print("Start calculating Mode " + str(i))
flag_continue = 0
ModePath = BaseName + "/Mode" + str(i)
if ParaIn['Continue']:
flag_continue = esutils.iscontinue(ModePath, "Mode", flag_se)
if flag_continue:
E = get_continue_mode_e(ModePath, E, i, flag_se)
else:
print(os.getcwd())
esutils.creat_folder(ModePath)
#os.chdir(ModePath)
for j in range(0, n_Strain):
print("Start calculating Strain " + str(StrainList[j]) + " in Mode " + str(i))
if j == int(n_Strain/2):
if flag_se == "e":
E[j, i-1] = E0[0]
elif flag_se == "s":
pass
else:
StrainPath = ModePath + "/Strain" + str(StrainList[j])
Strain = StrainList[j]/100.0
#print os.getcwd()
Eij = get_strain_e(ParaIn, StrainPath, StrainMode, BaseVec, Strain, i)
if flag_se == "e":
E[j, i-1] = Eij[0]
print("Energy:")
esutils.print_e(Eij)
elif flag_se == "s":
pass
os.chdir("../../../")
print("End of Strain " + str(StrainList[j]) + " in Mode " + str(i) + "\n")
os.chdir(ModePath)
if flag_se == "e":
np.savetxt(Efilename_Mode, E[:, i-1])
os.chdir("../../")
print("End of Mode " + str(i) + "\n")
np.savetxt(BaseName + "/EEnergy.txt", E)
print("\n==================Post Processing========================")
coef_fit = espost.get_coef(StrainList/100., E, V0, flag_se, 3)
print(coef_fit)
coef2 = coef_e.coef2
coef3 = coef_e.coef3
(C2, C3) = espost.get_cij(coef_fit, coef2, coef3, flag_se)
essym.print_cijk(CrystalType, 2)
print(C2)
essym.print_cijk(CrystalType, 3)
print(C3)
print("========================!!!END!!!=========================")
def elastic3():
#Print LOGO
esutils.print_logo()
#Read INPUT
if len(sys.argv) > 1:
INPUT = sys.argv[1]
else:
INPUT = "INPUT"
ParaIn = esutils.read_input(INPUT)
print("===================The input parameters===================")
esutils.print_parain(ParaIn)
#Import glue as eglue
eglue = __import__("energy." + ParaIn['EnergyCode'],
fromlist=ParaIn['EnergyCode'])
#Deform mode this is for cubic
#TODO : for any symmtry
Mode_index = range(1, 7)
#Get the energy run string
BaseName = ParaIn['BaseName']
if ParaIn['EnergyRun']:
RunStr = eglue.run(ParaIn['NP'], BaseName)
else:
RunStr = energy.glue.run()
#os.system(RunStr)
#Get the base vector
BaseVec = eglue.get_base_vec(BaseName)
print("====================Crystal Structure====================")
V0 = crylat.print_lattice(BaseVec)
#Calculate the energy of undeformed structure
# creat the folder Mode0
esutils.creat_folder(BaseName)
dstpath = BaseName + "/Mode0"
esutils.creat_folder(dstpath)
eglue.copy_files(BaseName, dstpath)
os.chdir(dstpath)
os.system(RunStr)
E0 = eglue.get_energy(BaseName)
os.chdir("../../")
print("Energy of undeformed structure:")
esutils.print_e(E0)
#print("\n")
print("\n==================Deformed Crystal========================")
StrainList = esutils.gen_strain_list(ParaIn)
n_Strain = len(StrainList)
n_Mode = len(Mode_index)
E = np.zeros((n_Strain, n_Mode))
#print E
for i in range(1, n_Mode + 1):
print("----------------------------------------------------------")
print("Start calculating Mode " + str(i))
ModePath = BaseName + "/Mode" + str(i)
esutils.creat_folder(ModePath)
for j in range(0, n_Strain):
print("Start calculating Strain " + str(StrainList[j]) +
" in Mode " + str(i))
if j == int(n_Strain / 2):
E[j][i - 1] = E0[0]
else:
StrainPath = ModePath + "/Strain" + str(StrainList[j])
esutils.creat_folder(StrainPath)
eglue.copy_files(BaseName, StrainPath)
os.chdir(StrainPath)
Strain = StrainList[j] / 100.0
StrainVerctor = crydef.deform_mode(Strain, i)
StrainMatrix = crydef.vec2matrix(StrainVerctor)
BaseVecNew = BaseVec.dot(
crydef.strain2deformgrad(StrainMatrix))
eglue.write_base_vec(BaseName, BaseVecNew)
os.system(RunStr)
Eij = eglue.get_energy(BaseName)
E[j][i - 1] = Eij[0]
crylat.print_lattice(BaseVecNew)
print("Energy:")
esutils.print_e(Eij)
os.chdir("../../../")
print("End of Strain " + str(StrainList[j]) + " in Mode " +
str(i) + "\n")
print("End of Mode " + str(i) + "\n")
np.savetxt(BaseName + "/EEnergy.txt", E)
print("\n==================Post Processing========================")
coef_fit = espost.get_coef(StrainList, E, V0)
print coef_fit
(C2, C3) = espost.get_cij(coef_fit, crystaltype)
print C2
print C3
print("========================!!!END!!!=========================")
def elastic3(INPUT="INPUT"):
#This is the main function for calculation
#Print LOGO
esutils.print_logo()
#Read INPUT
ParaIn = esutils.read_input(INPUT)
print("===================The input parameters===================")
esutils.print_parain(ParaIn)
flag_se = ParaIn['FlagSE'].lower()
EnergyCode = ParaIn['EnergyCode'].lower()
#Import first principles code module according to the EnergyCode settings in INPUT file
eglue = importlib.import_module('elastic3rd.energy.{}'.format(EnergyCode))
#Get some parameter's value from INPUT
CrystalType = ParaIn['CrystalType']
Ord = ParaIn['Ord']
CalMode = ParaIn['CalMode'].lower()
#Get the strain modes according to symmetry and order, the strain-stress method is under development
if CalMode == 's':
StrainIn = esutils.read_strainmode()
if flag_se == "e":
Cij_mode, coef_e, StrainMode = essym.CoefForSingleMode(
CrystalType, Ord, StrainIn)
elif flag_se == "s":
pass
elif CalMode == 'w':
if flag_se == "e":
coef_e, StrainMode = essym.gen_strain_mode(CrystalType, Ord)
elif flag_se == "s":
pass
#Get the strain list
StrainList = esutils.gen_strain_list(ParaIn)
n_Strain = len(StrainList)
n_Mode = StrainMode.shape[0]
#Init the energy
E = np.zeros((n_Strain, n_Mode))
if flag_se == "s":
E = np.zeros((n_Strain, 6 * n_Mode))
if flag_se == "e":
Efilename_Mode = "Energy_Mode.txt"
elif flag_se == "s":
Efilename_Mode = "Stress_Mode.txt"
#Get the energy run string
BaseName = ParaIn['BaseName']
if ParaIn['EnergyRun']:
RunStr = eglue.run(ParaIn['NP'], BaseName)
else:
RunStr = energy.glue.run()
#Get the base vector
BaseVec = eglue.get_base_vec(BaseName)
print("====================Crystal Structure====================")
V0 = crylat.print_lattice(BaseVec)
#Calculate the energy of undeformed structure
# creat the folder Mode0
dstpath = BaseName + "/Mode0"
E0 = get_strain_e(ParaIn, dstpath, StrainMode, BaseVec)
if CalMode == 's':
shutil.copyfile("STRAINMODE", BaseName + "/STRAINMODE")
#Begin the calculation of deformed structure
print("\n==================Deformed Crystal========================")
#Do a loop over the strain modes
for i in range(1, n_Mode + 1):
print("----------------------------------------------------------")
print("Start calculating Mode " + str(i))
flag_continue = 0
#Judge if this mode has been calculated or not
ModePath = BaseName + "/Mode" + str(i)
if ParaIn['Continue']:
flag_continue = esutils.iscontinue(ModePath, "Mode", flag_se)
if flag_continue:
#Calculated previously
E = get_continue_mode_e(ModePath, E, i, flag_se)
else:
#Not calculated yet, new calculations
print(os.getcwd())
esutils.creat_folder(ModePath)
#Do a loop over strain list
for j in range(0, n_Strain):
print("Start calculating Strain " + str(StrainList[j]) +
" in Mode " + str(i))
if j == int(n_Strain / 2):
#This is the un-deformed structure
if flag_se == "e":
E[j, i - 1] = E0[0]
elif flag_se == "s":
pass
else:
#Deformed structure
StrainPath = ModePath + "/Strain" + str(StrainList[j])
Strain = StrainList[j] / 100.0
#The judge on the continue mode is done in the following function
Eij = get_strain_e(ParaIn, StrainPath, StrainMode, BaseVec,
Strain, i)
if flag_se == "e":
E[j, i - 1] = Eij[0]
print("Energy:")
elif flag_se == "s":
pass
os.chdir("../../../")
print("End of Strain " + str(StrainList[j]) + " in Mode " +
str(i) + "\n")
os.chdir(ModePath)
if flag_se == "e":
np.savetxt(Efilename_Mode, E[:, i - 1])
os.chdir("../../")
print("End of Mode " + str(i) + "\n")
#Sve the energy
np.savetxt(BaseName + "/EEnergy.txt", E)
##Post process
print("\n==================Post Processing========================")
coef_fit = espost.get_coef(StrainList / 100., E, V0, flag_se, 3)
print(coef_fit)
coef2 = coef_e.coef2
coef3 = coef_e.coef3
(C2, C3) = espost.get_cij(coef_fit, coef2, coef3, flag_se)
essym.print_cijk(CrystalType, 2)
print(C2)
essym.print_cijk(CrystalType, 3)
print(C3)
print("========================!!!END!!!=========================")