auto

calc_manage.py

@@ -1846,14 +1846,17 @@ def inherit_icalc(inherit_type, it_new, ver_new, id_base, calc = None, st_base =
 
     new.len_units = 'Angstrom' #! Because from VASP
 
-
+    # print(id_base_st_type)
+    # sys.exit()
 
     new.version = ver_new
 
     if id_base_st_type == 'init':
         st = new.init
     elif id_base_st_type == 'end':
         st = new.end
+        if not hasattr(st, 'znucl'):
+            printlog('Error! end structure of', new.id, 'is empty! Use either init or finish calculation!')
 
     # print(st.typat)
 
@@ -2194,7 +2197,7 @@ def inherit_icalc(inherit_type, it_new, ver_new, id_base, calc = None, st_base =
 
 
 def res_loop(it, setlist, verlist,  calc = None, varset = None, analys_type = 'no', b_id = None, 
-    typconv='', up = "", imp1 = None, imp2 = None, matr = None, voronoi = False, r_id = None, readfiles = True, plot = True, show = '', 
+    typconv='', up = "", imp1 = None, imp2 = None, matr = None, voronoi = False, r_id = None, readfiles = True, plot = True, show = 'fo', 
     comment = None, input_geo_format = None, savefile = None, energy_ref = 0, ifolder = None, bulk_mul = 1, inherit_option = None,
     calc_method = None, u_ramping_region = None, input_geo_file = None, corenum = None, run = None, input_st= None,
     ortho = None, mat_proj_cell = None,

classes.py

@@ -72,6 +72,23 @@
 """
 
 
+class cd:
+    """Context manager for changing the current working directory"""
+    def __init__(self, newPath):
+        self.newPath = os.path.expanduser(newPath)
+
+    def __enter__(self):
+        self.savedPath = os.getcwd()
+        os.chdir(self.newPath)
+
+    def __exit__(self, etype, value, traceback):
+        os.chdir(self.savedPath)
+
+
+
+
+
+
 class Description():
     """
     Objects of this class include just folder and description of specific calculation.
@@ -2446,7 +2463,9 @@ def actualize_set(self, curset = None):
                 ns = len(spec_mom_is); 
                 number_of_ord = int(math.factorial(ns) / math.factorial(0.5 * ns)**2)
 
-                if 1:
+                if number_of_ord > 10000:
+                    printlog('Attention! Too much orderings (1000), skipping ...')
+                else:
                     nords = 10
                     use_each = number_of_ord // nords  # spin() should be improved to find the AFM state based on the number of configuration 
                     if use_each == 0:

geo.py

@@ -604,7 +604,7 @@ def ortho_vec(rprim, ortho_sizes = None):
 
 
 
-def create_supercell(st, mul_matrix, test_overlap = False, mp = 2, bound = 0.01): 
+def create_supercell(st, mul_matrix, test_overlap = False, mp = 4, bound = 0.01): 
     """ 
     st (Structure) -  
     mul_matrix (3x3 ndarray of int) - for example created by *ortho_    vec()* 

header.py

@@ -269,7 +269,9 @@ def runBash(cmd, env = None, detached = False):
     printlog('running in BASH:', cmd)
     my_env = os.environ.copy()
     # my_env["PATH"] = "/opt/local/bin:/opt/local/sbin:" + my_env["PATH"]
-    p = subprocess.Popen(cmd, executable='/bin/bash', shell=True, stdout=stdout, stderr = stderr, stdin = None, env = my_env)
+    p = subprocess.Popen(cmd, 
+        # executable='/bin/bash', 
+        shell=True, stdout=stdout, stderr = stderr, stdin = None, env = my_env)
     # print (cmd)
     # print 'Bash output is\n'+out
     # print ( str(out, 'utf-8') ) 
@@ -286,3 +288,17 @@ def runBash(cmd, env = None, detached = False):
 
 
 
+def run_win_cmd(cmd):
+    #example for windows
+    result = []
+    process = subprocess.Popen(cmd,
+                               shell=True,
+                               stdout=subprocess.PIPE,
+                               stderr=subprocess.PIPE)
+    for line in process.stdout:
+        result.append(line)
+    errcode = process.returncode
+    for line in result:
+        print(line)
+    if errcode is not None:
+        raise Exception('cmd %s failed, see above for details', cmd)

neb.py

@@ -3,16 +3,16 @@
 import copy, sys, os
 import numpy as np
 from operator import itemgetter
-
+import shutil
 
 from header import print_and_log, printlog, runBash
 import header
 from calc_manage import add_loop, res_loop, add_des, inherit_ngkpt
 from functions import  return_atoms_to_cell, push_to_server, invert
 from inout import write_xyz
 
-from small_functions import is_list_like
-from classes import CalculationVasp
+from small_functions import is_list_like, makedir
+from classes import CalculationVasp, cd
 from impurity import find_pores
 from tabulate import tabulate
 from geo import xcart2xred, xred2xcart, local_surrounding, replic, determine_symmetry_positions
@@ -735,9 +735,22 @@ def unique_by_key(elements, key=None):
 
     st1s.write_poscar('xyz/POSCAR1')
     st2s.write_poscar('xyz/POSCAR2')
-    a = runBash('cd xyz; '+header.PATH2NEBMAKE+' POSCAR1 POSCAR2 3')
     # print(a)
-    runBash('cd xyz; mkdir '+it_new+'_all;'+"""for i in {00..04}; do cp $i/POSCAR """+ it_new+'_all/POSCAR$i; done; rm -r 00 01 02 03 04')
+    # runBash('cd xyz; mkdir '+it_new+'_all;'+"""for i in {00..04}; do cp $i/POSCAR """+ it_new+'_all/POSCAR$i; done; rm -r 00 01 02 03 04')
+
+    with cd('xyz'):
+        a = runBash(header.PATH2NEBMAKE+' POSCAR1 POSCAR2 3')
+
+        dst = it_new+'_all'
+        makedir(dst)
+        for f in ['00', '01', '02', '03', '04']:
+            shutil.move(f+'/POSCAR', dst+'/POSCAR'+f)
+            shutil.rmtree(f)
+
+
+
+
+
     #prepare calculations
     # sys.exit()