auto

classes.py

@@ -5197,6 +5197,8 @@ def get_bader_ACF(self, p = 0):
         command1 = "cd "+path+"; ~/tools/vts/chgsum.pl "+AECCAR0+" "+AECCAR2+"; "+\
         "mv CHGCAR_sum "+CHGCAR_sum+";" # on cluster
 
+        command_chg_gunzip = 'gunzip '+CHG+'.gz ' # on cluster
+
         command2 = "rsync "+CHG_scratch_gz+' '+path+' ; gunzip '+CHG+'.gz ' # on cluster
 
         mv = v+".bader.log; mv ACF.dat "+v+".ACF.dat; mv AVF.dat "+v+".AVF.dat; mv BCF.dat "+v+".BCF.dat; cat "+v+".bader.log"
@@ -5210,11 +5212,18 @@ def get_bader_ACF(self, p = 0):
         command_cat_ACF    = " cat "+path+v+".ACF.dat"
         # run_on_server()
 
+
+        #Calculate CHGCAR_sum
         if run_on_server(command_check_CHG_sum, self.cluster_address): 
             print_and_log(  CHGCAR_sum, "does not exist. trying to calculate it ", imp = 'Y')
             printlog( run_on_server(command1, self.cluster_address)+'\n', imp = 'Y' ) 
         # sys.exit()
 
+        #Check chgcar
+        if run_on_server(command_check_CHG, self.cluster_address): #true if file not exists
+            printlog( 'Warning! File ', CHG, "does not exist. Checking .gz .. ", imp = 'Y')
+
+            printlog( run_on_server(command_chg_gunzip, self.cluster_address)+'\n', imp = 'y' ) 
 
         if run_on_server(command_check_CHG, self.cluster_address): #true if file not exists
             printlog( 'Warning! File ', CHG, "does not exist. Trying to restore it from archive .. ", imp = 'Y')

project_template/project_conf.py

@@ -43,8 +43,10 @@
 'vasp_com':'mpirun  vasp_std',
 'homepath':'/home/Dmitry.Aksenov/',
 'schedule':'PBS',
+'walltime':72,
 'corenum':16,
-'pythonpath':'/usr/lib64/python2.7/site-packages/numpy'
+'pythonpath':'/usr/lib64/python2.7/site-packages/numpy',
+'modules':'module load Compilers/Intel/psxe_2015.6; module load MPI/intel/5.1.3.258/intel; module load QCh/VASP/5.4.1p1/psxe2015.6; module load ScriptLang/python/2.7',
 }
 
 CLUSTERS['bsu'] = {'address':'[email protected]',

tutorials/Bi2Se3/Bi2Se3.bader/1.CONTCAR

@@ -0,0 +1,19 @@
+i2a=[Bi,Se] ; Bi2Se3_mp-541837_computed 
+   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
+  0.3984349999999992  0.3984349999999992  0.3984349999999992
+  0.6015650000000008  0.6015650000000008  0.6015650000000008
+  0.0000000000000000  0.0000000000000000  0.0000000000000000
+  0.2157150000000030  0.2157150000000030  0.2157150000000030
+  0.7842849999999970  0.7842849999999970  0.7842849999999970
+
+  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.bader/1.POSCAR

@@ -0,0 +1,13 @@
+i2a=[Bi,Se] ; Bi2Se3_mp-541837_computed
+ 1.000000000000000
+  4.103097   0.000000   9.409867
+  1.962329   3.603424   9.409867
+  0.000000   0.000000  10.265525
+Bi Se 
+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.bader/Bi2Se3.bader.run

@@ -0,0 +1,32 @@
+#!/bin/bash   
+#SBATCH -J Bi2Se3.bader
+#SBATCH -t 250:00:00 
+#SBATCH -N 1
+#SBATCH -n 16
+#SBATCH -o /home/aksenov/topologic/Bi2Se3//Bi2Se3.bader/sbatch.out
+#SBATCH -e /home/aksenov/topologic/Bi2Se3//Bi2Se3.bader/sbatch.err
+#SBATCH --mem-per-cpu=7675
+cd /home/aksenov/topologic/Bi2Se3//Bi2Se3.bader/
+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.bader.1.log
+sleep 20
+mv OUTCAR 1.OUTCAR
+mv CONTCAR 1.CONTCAR
+cp CHGCAR 1.CHGCAR
+gzip -f 1.CHGCAR
+mv AECCAR0 1.AECCAR0
+mv AECCAR2 1.AECCAR2
+mv vasprun.xml 1.vasprun.xml
+rm WAVECAR  # rm_chg_wav flag
+
+#Footer section: 
+rm PROCAR DOSCAR OSZICAR PCDAT REPORT XDATCAR vasprun.xml
+rm RUNNING

tutorials/Bi2Se3/Bi2Se3.bader/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.bader/INCAR

@@ -0,0 +1,27 @@
+SYSTEM =  auto add_des ; no description for these set, see history
+ADDGRID = .TRUE.
+ALGO = Normal
+EDIFF = 1e-08
+EDIFFG = 0
+ENAUG = 776.16
+ENCUT = 441.0
+IBRION = 1
+ICHARG = 1
+ISIF = 2
+ISMEAR = 2
+ISTART = 0
+KGAMMA = .TRUE.
+LAECHG = .TRUE.
+LPLANE = .TRUE.
+LREAL = Auto
+LSCALU = .FALSE.
+MAXMIX = 40
+NBANDS = 38
+NELM = 100
+NELMIN = 4
+NPAR = 1
+NSIM = 4
+NSW = 0
+PREC = Accurate
+SIGMA = 0.2
+

tutorials/Bi2Se3/Bi2Se3.bader/KPOINTS

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

tutorials/Configure.ipynb

@@ -1,7 +1,7 @@
 {
  "metadata": {
   "name": "",
-  "signature": "sha256:443892cd776f9de1ef7d55829a60f6c3a1ae1169187dd95cdb26451b04b9efcd"
+  "signature": "sha256:739a52c62ead6d3e233e7d5792bf2d9d596d60be0adae4bfad6615088c246d57"
  },
  "nbformat": 3,
  "nbformat_minor": 0,
@@ -58,7 +58,11 @@
       "'pythonpath':'/usr/lib64/python2.7/site-packages/numpy',\n",
       "'vasp_com':'prun /opt/vasp/bin/vasp5.4.1MPI',  # path to vasp binary\n",
       "#optional parameters:\n",
-      "'sshpath':True # use sshpath in rsync commands \n",
+      "'sshpath':True # use sshpath in rsync commands\n",
+      "'modules':'module load Compilers/Intel/psxe_2015.6; \\\n",
+      "           module load MPI/intel/5.1.3.258/intel; \\\n",
+      "           module load QCh/VASP/5.4.1p1/psxe2015.6; \\\n",
+      "           module load ScriptLang/python/2.7' # additional commands for PBS script, such as load of moudli\n",
       "}\n",
       "\n"
      ],