Merge pull request #11 from MDIL-SNU/python3

Python3

docs/Output/Output.rst

@@ -86,7 +86,7 @@ Results
     - Band_gap_hybrid_GGA.log: 
         Information of band gap with HSE@PBE scheme
 
-    - dos_GGA.pnd (dos_GGA.pdf): 
+    - dos_GGA.png (dos_GGA.pdf): 
         Density of states image
 
     - dielectric_GGA.log: 
@@ -117,4 +117,4 @@ name_with_U
     If the material is metallic and DFT+U calculation has been conducted,
     all of results move to this directory.
 
-Additionally, AMP\ :sup:`2`\  provides log file as amp2.log for tracing the calculation.
+Additionally, AMP\ :sup:`2`\  provides log file as amp2.log for tracing the calculation.

src/amp2_input.py

@@ -2,7 +2,7 @@
 ### Date: 2019-04-08			###
 ### yybbyb@snu.ac.kr			###
 ###########################################
-import math, glob, os, shutil, sys, subprocess
+import math, os, shutil, sys, subprocess
 import yaml
 from module_vasprun import wincar,incar_from_yaml
 from module_log import *

src/band.py

@@ -34,7 +34,8 @@
 
 pot_type = sys.argv[5]
 if pot_type == 'LDA':
-    POT = 'LDA'
+pin
+/spinPOT = 'LDA'
 else:
     POT = 'GGA'
 

src/config_def.yaml

@@ -15,16 +15,16 @@ program:
   mpi_command: mpirun
 
 calculation:
-  kp_test: 1
-  encut_test: 1
-  relaxation: 1
-  band: 1
-  density_of_states: 1
-  hse_oneshot: 1
-  dielectric: 1
-  effective_mass: 1
-  plot: 1
-  magnetic_ordering: 1
+  kp_test: T
+  encut_test: T
+  relaxation: T
+  band: T
+  density_of_states: T
+  hse_oneshot: T
+  dielectric: T
+  effective_mass: T
+  plot: T
+  magnetic_ordering: T
   large_off: -1
 
 cif2vasp:

src/module_band.py

@@ -678,7 +678,7 @@ def gap_estimation(target,fermi,spin,ncl,KPT,Band,nelect):
 		gap_simple.write('     metal\n')
 		if metal == 2 :
 			gap_log.write('! If it is not hybrid calculation, additional search is required for hybrid calculation.\n')
-			gap_simple.write('! If it is not hybrid calculation, Additional search is required for hybrid calculation.\n')
+			gap_simple.write('! If it is not hybrid calculation, additional search is required for hybrid calculation.\n')
 		else :
 			gap_log.write("Use the 'KPT' file for hybrid calculation\n")
 			kpt_out.write("Example file\n               0\nReciprocal\n")
@@ -793,3 +793,24 @@ def band_warning(Band,target):
 			make_amp2_log(target,'\tIndex of kpts: '+str(warn_list[0]+1)+'\t from '+str(warn_list[1][0]+1)+' th band')
 
 	return warn
+
+def check_half_metal(target):
+	spin = pygrep('ISPIN',target+'/OUTCAR',0,0).split()[2]
+	ncl = pygrep('NONCOL',target+'/OUTCAR',0,0).split()[2]
+	if not (spin == '2' and ncl =='F'):
+		half_metal = 0
+	else:
+		[KPT,Band,nelect] = EIGEN_to_array(target+'/EIGENVAL',spin)
+		fermi = get_fermi_level(Band,nelect,ncl)
+		half_metal = 0
+		for i in range(int(spin)) :
+			metal = 0
+			for n in range(len(Band)) :
+				single_band = [Band[n][x][i] for x in range(len(KPT))]
+				band_max = max(single_band)
+				band_min = min(single_band)
+				if band_max > fermi and band_min < fermi:
+					metal = 1
+			if metal = 0:
+				half_metal = 1
+	return half_metal

src/module_vasprun.py

@@ -326,7 +326,7 @@ def make_multiple_kpts(kp_log,kpt_file,pos_file,kp_multi,sym,gam_option):
 		KP_ori = khead[3].split()
 		KP=[]
 		for i in range(3) :
-			if sym == 5 or sym == 6:
+			if sym in [5,6,10]:
 				KP.append(str(max([int(x) for x in KP_ori[i]])*kp_multi))
 			else:
 				KP.append(str(int(KP_ori[i])*kp_multi))

src/rerun_for_metal.py

@@ -8,6 +8,7 @@
 from input_conf import input_conf
 from module_amp2_input import *
 from module_log import *
+from module_band import check_half_metal
 from input_conf import set_on_off
 from _version import __version__
 code_data = 'Version '+__version__+'. Modified at 2020-01-15'
@@ -54,6 +55,16 @@
 if U_on == 0 :
 	sys.exit()
 
+# Check half metal
+if os.path.isfile(target+'/band_GGA/Band_gap.log'):
+	if check_half_metal(target+'/band_GGA') == 1:
+		sys.exit()
+elif os.path.isfile(target+'/band_LDA/Band_gap.log'):
+	if check_half_metal(target+'/band_LDA') == 1:
+		sys.exit()
+else:
+	sys.exit()
+
 # Backup +U calculation results
 backup_path = target+'/'+target.split('/')[-1]+'_with_U'
 if not os.path.isdir(backup_path):