def getEnergyConfig(X, structEq):
import potential
from potential import VLJ as V
import harmonic as ha
# E = 0.5*(random() - 0.5) - 161.895
# energyPerParticle = 0
# E, energyPerParticle = ha.get3DPotNearFirstNeighb(X, V, a1, a2, a3)
#
# # E = potential.getTotalPotentialEnergy(X, V2)
# # E = potential.get3DPotNearFirstNeighb(X, V, a1, a2, a3)
# # E = 0.2*(random()-0.5) - 0.56 # <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
# # print(E)
# # E = getEnergyFromStaticMTP(X) # do not relax! <<<<<<<<<<<<<<<<<<<<<<<<<<<
import crystal as cr
import numpy as np
from numpy import linalg as LA
import copy
# structX = cr.getFccEquilibrium()
structX = copy.deepcopy(structEq)
for i in range(structEq.num_sites):
structX[i] = structX[i].specie, np.array(X[i]) ## X[i] must be in FRACTIONAL COORDINATES!!!
# dist = LA.norm(structX[i].frac_coords - np.array(X[i]))
# if (dist > -0.1):
# Xtemp = cr.getFccEquilibrium()
# print(i)
# print(Xtemp[i].frac_coords)
# print(structX[i].frac_coords)
# print(X[i])
# 1.3
radio = 3.3 * structX[0].distance(structX[1]) # for first nearest neighbors
dRneighborsFromEachSite = cr.getDRneighborsFromEachSite(structX, radio)
assert(len(dRneighborsFromEachSite) != 0)
# for i in range(structEq.num_sites):
# assert( len(structEq.get_neighbors(structEq[i], radio, include_index=True)) == 12 )
#
E = cr.getEnergy(structX, radio, dRneighborsFromEachSite)
# print(E)
# E = 0.5*(random() - 0.5) - 161.895
# energyPerParticle = 0
# energyPerParticle = 0
# return E, energyPerParticle
return E, 0
def getEnergyConfig(structX, radio, dRneighborsFromEachSite):
import potential
from potential import VLJ as V
# import harmonic as ha
import crystal as cr
# E = 0
# E, energyPerParticle = ha.get3DPotNearFirstNeighb(structX, V, a1, a2, a3)
energy = cr.getEnergy(structX, radio, dRneighborsFromEachSite)
# E = potential.getTotalPotentialEnergy(X, V2)
# E = potential.get3DPotNearFirstNeighb(X, V, a1, a2, a3)
# E = 0.2*(random()-0.5) - 0.56 # <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
# print(E)
# E = getEnergyFromStaticMTP(X) # do not relax! <<<<<<<<<<<<<<<<<<<<<<<<<<<
return energy
import crystal as cr import numpy as np # Get names and equilibrium positions of atoms: # you will need to find first the equilibrium positions when having `V` # For the project, MTP or DFT?? will give the equilibrium positions. # lAtomsEquilibrium, a1, a2, a3 = potential.getAtomsAtEquilibriumPositions() # Xeq, a1, a2, a3, Emin, forceMatrix = ha.getConfigEquilibrium() # structEq = cr.getStruct() # to be used from cfg of mtp structEq = cr.getFccEquilibrium() radio = 1.1 * structEq[0].distance(structEq[1]) # for first nearest neighbors Emin = cr.getEnergy(structEq, radio, []) indxNeigsFromEachSite = cr.getIndxNeigsFromEachSite(structEq, radio) dRneighborsFromEachSite = cr.getDRneighborsFromEachSite(structEq, radio) forceMatrix = cr.getForceMatrix(structEq, indxNeigsFromEachSite, dRneighborsFromEachSite, radio) Emin # forceMatrix # structEq.num_sites # # structEq[0].coords # structEq[0].y # # structEq[0].coords + structEq[0].coords # # structEq[0].coords = structEq[0].coords + np.array([10,20,30]) #