auto

set_functions.py

@@ -100,7 +100,7 @@
 'set_sequence'# sequence of sets
 ]
 
-def read_vasp_sets(varset, user_vasp_sets, override_global = False):
+def read_vasp_sets(user_vasp_sets, override_global = False):
     """
     Read user sets and add them to project database
     Now for VASP
@@ -117,6 +117,10 @@ def read_vasp_sets(varset, user_vasp_sets, override_global = False):
     # varset['9'].printme()
     # print varset['9ml'].history
     # print varset['9'].history
+
+    varset = header.varset
+
+
     vasp_keys = vasp_electronic_keys+vasp_ionic_keys+vasp_other_keys
     bfolder = '' #by default no blockfolder
     for l in user_vasp_sets:
@@ -183,7 +187,7 @@ def read_vasp_sets(varset, user_vasp_sets, override_global = False):
 
 
 
-
+        header.varset = varset
 
     return varset
 
@@ -258,9 +262,9 @@ def __init__(self, ise, path_to_potcar = None):
     def printme(self):
         for key in self.vasp_params:
             if self.vasp_params[key] == None: continue
-            print_and_log( "{:30s} = {:s} ".format("s.vasp_params['"+key+"']", str(self.vasp_params[key]) ) )
+            print_and_log( "{:30s} = {:s} ".format("s.vasp_params['"+key+"']", str(self.vasp_params[key]) ), imp = 'Y', end = '\n' )
 
-        print_and_log('POTDIR:', self.potdir)
+        print_and_log('POTDIR:', self.potdir, imp = 'Y', end = '\n' )
 
     def update(self):
         #deprecated, but still can be usefull

tutorials/Bi2Se3/Bi2Se3.ion_relax/1.CONTCAR

@@ -0,0 +1,19 @@
+i2a=[Bi,Se] ; Bi2Se3.ion_relax.1        
+   1.00000000000000     
+     4.1030970000000000    0.0000000000000000    9.4098670000000002
+     1.9623290000000000    3.6034240000000000    9.4098670000000002
+     0.0000000000000000    0.0000000000000000   10.2655250000000002
+   Bi   Se
+     2     3
+Direct
+  0.3982239088657034  0.3982239088657034  0.3982239088657034
+  0.6017760911342980  0.6017760911342980  0.6017760911342980
+  0.0000000000000000 -0.0000000000000000 -0.0000000000000000
+  0.2162381922773176  0.2162381922773176  0.2162381922773176
+  0.7837618077226826  0.7837618077226826  0.7837618077226826
+
+  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00

tutorials/Bi2Se3/Bi2Se3.ion_relax/1.POSCAR

@@ -0,0 +1,12 @@
+i2a=[Bi,Se] ; Bi2Se3.ion_relax.1
+ 1.000000000000000
+  4.103097   0.000000   9.409867
+  1.962329   3.603424   9.409867
+  0.000000   0.000000  10.265525
+2 3 
+Direct
+  0.3984350000000000  0.3984350000000000  0.3984350000000000
+  0.6015650000000000  0.6015650000000000  0.6015650000000000
+  0.0000000000000000  0.0000000000000000  0.0000000000000000
+  0.2157150000000000  0.2157150000000000  0.2157150000000000
+  0.7842850000000000  0.7842850000000000  0.7842850000000000

tutorials/Bi2Se3/Bi2Se3.ion_relax/Bi2Se3.ion_relax.1.cif

@@ -0,0 +1,64 @@
+# generated using pymatgen
+data_Bi2Se3
+_symmetry_space_group_name_H-M   R-3m
+_cell_length_a   4.19136659
+_cell_length_b   4.19136659
+_cell_length_c   29.92868771
+_cell_angle_alpha   90.00000000
+_cell_angle_beta   90.00000000
+_cell_angle_gamma   120.00000000
+_symmetry_Int_Tables_number   166
+_chemical_formula_structural   Bi2Se3
+_chemical_formula_sum   'Bi6 Se9'
+_cell_volume   455.333496814
+_cell_formula_units_Z   3
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+  2  '-x, -y, -z'
+  3  '-y, x-y, z'
+  4  'y, -x+y, -z'
+  5  '-x+y, -x, z'
+  6  'x-y, x, -z'
+  7  'y, x, -z'
+  8  '-y, -x, z'
+  9  'x-y, -y, -z'
+  10  '-x+y, y, z'
+  11  '-x, -x+y, -z'
+  12  'x, x-y, z'
+  13  'x+2/3, y+1/3, z+1/3'
+  14  '-x+2/3, -y+1/3, -z+1/3'
+  15  '-y+2/3, x-y+1/3, z+1/3'
+  16  'y+2/3, -x+y+1/3, -z+1/3'
+  17  '-x+y+2/3, -x+1/3, z+1/3'
+  18  'x-y+2/3, x+1/3, -z+1/3'
+  19  'y+2/3, x+1/3, -z+1/3'
+  20  '-y+2/3, -x+1/3, z+1/3'
+  21  'x-y+2/3, -y+1/3, -z+1/3'
+  22  '-x+y+2/3, y+1/3, z+1/3'
+  23  '-x+2/3, -x+y+1/3, -z+1/3'
+  24  'x+2/3, x-y+1/3, z+1/3'
+  25  'x+1/3, y+2/3, z+2/3'
+  26  '-x+1/3, -y+2/3, -z+2/3'
+  27  '-y+1/3, x-y+2/3, z+2/3'
+  28  'y+1/3, -x+y+2/3, -z+2/3'
+  29  '-x+y+1/3, -x+2/3, z+2/3'
+  30  'x-y+1/3, x+2/3, -z+2/3'
+  31  'y+1/3, x+2/3, -z+2/3'
+  32  '-y+1/3, -x+2/3, z+2/3'
+  33  'x-y+1/3, -y+2/3, -z+2/3'
+  34  '-x+y+1/3, y+2/3, z+2/3'
+  35  '-x+1/3, -x+y+2/3, -z+2/3'
+  36  'x+1/3, x-y+2/3, z+2/3'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Bi  Bi1  6  0.000000  0.000000  0.398224  1
+  Se  Se2  6  0.000000  0.000000  0.216238  1
+  Se  Se3  3  0.333333  0.666667  0.666667  1

tutorials/Bi2Se3/Bi2Se3.ion_relax/Bi2Se3.ion_relax.run

@@ -0,0 +1,28 @@
+#!/bin/bash   
+#SBATCH -J Bi2Se3.ion_relax
+#SBATCH -t 250:00:00 
+#SBATCH -N 1
+#SBATCH -n 16
+#SBATCH -o /home/aksenov/topologic/Bi2Se3//Bi2Se3.ion_relax/sbatch.out
+#SBATCH -e /home/aksenov/topologic/Bi2Se3//Bi2Se3.ion_relax/sbatch.err
+#SBATCH --mem-per-cpu=7675
+cd /home/aksenov/topologic/Bi2Se3//Bi2Se3.ion_relax/
+export OMP_NUM_THREADS=1
+module add prun/1.0
+module add intel/16.0.2.181
+module add impi/5.1.3.181
+export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/aksenov/tools/lib64:/home/aksenov/tools/atlas
+export PATH=$PATH:/home/aksenov/tools
+touch RUNNING
+#Basic run:
+cp 1.POSCAR POSCAR
+prun /opt/vasp/bin/vasp5.4.1MPI >Bi2Se3.ion_relax.1.log
+sleep 20
+mv OUTCAR 1.OUTCAR
+mv CONTCAR 1.CONTCAR
+cp CHGCAR 1.CHGCAR
+gzip -f 1.CHGCAR
+
+#Footer section: 
+rm PROCAR DOSCAR OSZICAR PCDAT REPORT XDATCAR vasprun.xml
+rm RUNNING

tutorials/Bi2Se3/Bi2Se3.ion_relax/Bi2Se3_mp-541837_computed.POSCAR

@@ -0,0 +1,13 @@
+Bi2 Se3
+1.0
+4.103097 0.000000 9.409867
+1.962329 3.603424 9.409867
+0.000000 0.000000 10.265525
+Bi Se
+2 3
+direct
+0.398435 0.398435 0.398435 Bi
+0.601565 0.601565 0.601565 Bi
+0.000000 0.000000 0.000000 Se
+0.215715 0.215715 0.215715 Se
+0.784285 0.784285 0.784285 Se

tutorials/Bi2Se3/Bi2Se3.ion_relax/INCAR

@@ -0,0 +1,25 @@
+SYSTEM = Bi2 Se3 auto add_des ; no description for these set, see history
+
+ALGO = Normal
+EDIFF = 6e-06
+EDIFFG = 0
+ENAUG = 776.16
+ENCUT = 441.0
+IBRION = 1
+ISIF = 2
+ISMEAR = 2
+ISTART = 0
+KGAMMA = .TRUE.
+LPLANE = .TRUE.
+LREAL = Auto
+LSCALU = .FALSE.
+MAXMIX = 40
+NBANDS = 38
+NELM = 50
+NELMIN = 4
+NPAR = 1
+NSIM = 4
+NSW = 20
+PREC = Normal
+SIGMA = 0.2
+

tutorials/Bi2Se3/Bi2Se3.ion_relax/KPOINTS

@@ -0,0 +1,5 @@
+Automatic Mesh
+0 
+Gamma
+8 8 8 
+0 0 0