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dimonaks · Oct 26, 2018 · ece45be · ece45be
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commit ece45be
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Showing 4 changed files with 13 additions and 7 deletions.
diff --git a/siman/classes.py b/siman/classes.py
@@ -4516,15 +4516,21 @@ def read_results(self, load = '', out_type = '', voronoi = False, show = '', cho
                     if "in kB" in line:
                         # print(line)
                         line = line.replace('-', ' -')
-
-                        self.stress = [float(i)*100 for i in line.split()[2:]]  # in MPa 
+                        # print(line)
+                        if '*' in line:
+                            self.stress = [0,0,0] # problem with stresses
+                            printlog('Warning! Some problem with *in kB* line of OUTCAR')
+                        else:
+                            self.stress = [float(i)*100 for i in line.split()[2:]]  # in MPa 
                     if "Total  " in line:
                         # print(line)
                         line = line.replace('-', ' -')
                         try:
                             self.intstress = [int(float(i)*1000) for i in line.split()[1:]] #stress in internal units; can be regarded as forces
                         except:
                             self.intstress = [0,0,0]
+                            printlog('Warning! Some problem with *Total * line of OUTCAR')
+
                     if "external pressure =" in line: 
                         #print iterat
                         self.extpress = float(line.split()[3]) * 100 # in MPa 

diff --git a/siman/monte_functions.py b/siman/monte_functions.py
@@ -21,15 +21,15 @@ def metropolis(E1, E2, T = 1):
     """
     decrease = False # energy reduction
 
-    # kb = 1.3806488*10**-23  / 1.6 * 10 **19
+    # kB = 1.3806488*10**-23  / 1.6 * 10 **19
     dE = E2 - E1
 
     printlog("metropolis(): dE is ", dE)
     if dE < -0.000001:
         printlog( "dE is ", dE, "Accept!")
         decrease = True
-    elif  1 > math.exp(-dE/kb/T) > random():
-        printlog ("Accepted due to the temperature; exponent is ", math.exp(-dE/kb/T) )
+    elif  1 > math.exp(-dE/kB/T) > random():
+        printlog ("Accepted due to the temperature; exponent is ", math.exp(-dE/kB/T) )
         decrease = True
     else:
         printlog('Not accepted')

diff --git a/siman/picture_functions.py b/siman/picture_functions.py
@@ -53,7 +53,7 @@ def plot_mep(atom_pos, mep_energies, image_name = None, filename = None, show =
     """
 
 
-    from analysis import determine_barrier
+    from siman.analysis import determine_barrier
 
     if filename is None:
         filename = image_name

diff --git a/siman/project_funcs.py b/siman/project_funcs.py
@@ -3832,7 +3832,7 @@ def process_cathode_material(projectname, step = 1, target_x = 0, update = 0, pa
 
 
     """
-    from geo import determine_symmetry_positions, primitive, remove_x
+    from siman.geo import determine_symmetry_positions, primitive, remove_x
     pn = projectname
 
     m_set = '1u'; n_set  = '1u'; clust = 'cee' #