本文整理汇总了Python中framework.Framework.update_UC_matrix方法的典型用法代码示例。如果您正苦于以下问题：Python Framework.update_UC_matrix方法的具体用法？Python Framework.update_UC_matrix怎么用？Python Framework.update_UC_matrix使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类framework.Framework的用法示例。
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示例1: Assembly
# 需要导入模块: from framework import Framework [as 别名]
# 或者: from framework.Framework import update_UC_matrix [as 别名]
#.........这里部分代码省略.........
b = self.cxn_xyz[i]
M = trans.affine_matrix_from_points(a, b, shear = False, scale = False, usesvd = True)
alpha, beta, gamma = trans.euler_from_matrix(M)
translations = M[0:3,3]
conn_start_ind = 1 + len(self.rods) + i*6
self.opt_vec[conn_start_ind+0] = alpha
self.opt_vec[conn_start_ind+1] = beta
self.opt_vec[conn_start_ind+2] = gamma
self.opt_vec[conn_start_ind+3] = translations[0]
self.opt_vec[conn_start_ind+4] = translations[1]
self.opt_vec[conn_start_ind+5] = translations[2]
print(M)
def construct_curr_UC(self, xuse):
"""
Creates the current representation of the unit cell so that we can
evaluate how well the components are embedded in 3 space
NOTE: we may have to break this optimization into several pieces:
(1) determine embedding by fitting one molecule
(2) only optimize the remaining molecule orientations/translations with the fixed
embedding variables (F, {dCs})
"""
# Steps to reconstruct unit cell
# 1: stasrt with opt_vec[0] (F) and opt_vec[1:n_rods] (set of dCs)
# 2: recompute cxn points based on F and dCs
# recompute UC matrix transformation based on current scale factor
to_cartesian = self.frame.update_UC_matrix(xuse[0], self.twod_direct)
to_fractional = np.linalg.inv(to_cartesian)
# get the current oriented and translated ligands
oriented = self.orient_cxn_and_translate(xuse)
# get final connection pt coords on molecule
for i in range(len(oriented)):
oriented[i][0:3,:] = np.dot(to_fractional, oriented[i][0:3,:])
oriented[i][0:3,:] = self.frame.modGroupUC(oriented[i][0:3,:])
oriented[i][0:3,:] = np.dot(to_cartesian, oriented[i][0:3,:])
final_xyz = []
#new_abc = np.copy(self.cxn_ref_abc)
#print(new_abc)
#print(np.shape(new_abc))
#print(self.cxn_ref_abc)
#print(np.shape(self.cxn_ref_abc))
# get final connection pt coords on rod
for i in range(len(self.cxns)):
this_new_abc = np.copy(self.cxn_ref_abc[i])
conn_start_ind = 1 + len(self.rods) + i*6 + i*len(self.cxns[i])
for j in range(len(self.cxns[i])):
# shift ref pt based on curr val of rod shift
# print(xuse[1 + self.connect_to_rod[i][j]])
this_new_abc[self.oned_direct,j] += xuse[1 + self.connect_to_rod[i][j]]