Merge pull request #20 from MDIL-SNU/src_1.0.0

Better algorithm for magnetism

src/_version.py

@@ -1 +1 @@
-__version__ = "0.9.6"
+__version__ = "1.0.0"

src/band.py

@@ -1,6 +1,6 @@
 ###########################################
-### Date: 2018-12-05            ###
-### yybbyb@snu.ac.kr            ###
+### Date: 2020-11-05                    ###
+### mk01071@snu.ac.kr                   ###
 ###########################################
 # This is for drawing band structure and estimating band gap.
 import shutil, os, sys, subprocess, yaml
@@ -10,7 +10,7 @@
 from module_hse import *
 from input_conf import set_on_off
 from _version import __version__
-code_data = 'Version '+__version__+'. Modified at 2020-05-12'
+code_data = 'Version '+__version__+'. Modified at 2020-11-05'
 
 # Set input
 dir = sys.argv[1]
@@ -133,8 +133,11 @@
         else:
             mag_on = check_magnet(dir+'/relax_'+pot_type,inp_yaml['magnetic_ordering']['minimum_moment'])
         vasprun = make_incar_for_ncl(dir_band,mag_on,kpar,npar,vasp_std,vasp_gam,vasp_ncl)
-        wincar(dir_band+'/INCAR',dir_band+'/INCAR',[['NSW','0'],['LCHARG','.T.'],['ALGO','Normal']],[])
+        wincar(dir_band+'/INCAR',dir_band+'/INCAR',[['NSW','0'],['LCHARG','.T.']],[])
 
+        if os.path.isfile(dir+'/relax_'+pot_type+'/CHGCAR') and os.path.getsize(dir+'/relax_'+pot_type+'/CHGCAR') > 1000: #If electronic convergence in previous step had problem
+            shutil.copyfile(dir+'/relax_'+pot_type+'/CHGCAR',dir_band+'/CHGCAR')
+            wincar(dir_band+'/INCAR',dir_band+'/INCAR',[['ICHARG','1']],[])
         # VASP calculation for CHGCAR
         out = run_vasp(dir_band,nproc,vasprun,mpi)
         if out == 1:  # error in vasp calculation

src/cutoff.py

@@ -1,15 +1,16 @@
 ####################################
-# date : 2018-12-06                #
+# date : 2020-11-05                #
 # Author : feihoon@snu.ac.kr       #
 # Modifier : yybbyb@snu.ac.kr      #
+# Modifier : mk01071@snu.ac.kr     #
 ####################################
-import os, sys, subprocess, yaml
+import os, sys, subprocess, yaml, shutil
 from module_log import *
 from module_vasprun import *
 from module_converge import *
 import math
 from _version import __version__
-code_data = 'Version '+__version__+'. Modified at 2020-05-12'
+code_data = 'Version '+__version__+'. Modified at 2020-11-05'
 
 # Set input
 dir = sys.argv[1]
@@ -105,6 +106,8 @@
 			incar_for_hse(now_path+'/INCAR')
 		incar_from_yaml(now_path,inp_conv['incar'])
 		wincar(now_path+'/INCAR',now_path+'/INCAR',[['ENCUT',str(ENCUT)],['NSW','0'],['LWAVE','F'],['LCHARG','F']],[])
+		if pygrep('ALGO',dir+'/cutoff/EN'+str(ENCUT)+"/INCAR",0,0).split()[2].upper()[0] == "A" or (ENCUT-ENSTEP>=EN_recommend and os.path.isfile(dir+'/cutoff/EN'+str(ENCUT-ENSTEP)+"/INCAR") and pygrep('ALGO',dir+'/cutoff/EN'+str(ENCUT-ENSTEP)+"/INCAR",0,0).split()[2].upper()[0] == "A"): 
+			wincar(now_path+'/INCAR',now_path+'/INCAR',[['NSW','0'],["ALGO","All"],['LCHARG','T'],['LWAVE','F']],[])
 		# Running vasp
 		out = run_vasp(now_path,nproc,vasprun,mpi)
 		if ENCUT < EN_recommend:
@@ -146,9 +149,32 @@
 				out = electronic_step_convergence_check(now_path)
 
 			if out == 2:  # electronic step is not converged. (algo = normal)
-				make_amp2_log(dir+'/cutoff','The calculation stops but electronic step is not converged.')
-				print(0)
-				sys.exit()
+#				make_amp2_log(now_path,'We change ALGO normal to All.')
+#				wincar(now_path+'/INCAR',now_path+'/INCAR',[['ALGO','All'],['NSW','0'],['LCHARG','T'],['LWAVE','F'],['AMIX','#'],['BMIX','#'],['AMIX_MAG','#'],['BMIX_MAG','#']],[])
+				make_amp2_log(now_path,'We try ALGO All with a better guess on initial charge density.')
+				wincar(now_path+'/INCAR',now_path+'/INCAR',[['ALGO','All'],['NSW','0'],['LCHARG','T'],['LWAVE','F'],['AMIX','#'],['BMIX','#'],['AMIX_MAG','#'],['BMIX_MAG','#']],[])
+				if os.path.isfile(now_path+'/CHGCAR') and os.path.getsize(now_path+'/CHGCAR') > 1000:
+					wincar(now_path+'/INCAR',now_path+'/INCAR',[['ICHARG','1']],[])
+				out = run_vasp(now_path,nproc,vasprun,mpi)
+				if out == 1: # error in vasp calculation
+					print(0)
+					sys.exit()
+				else:
+					out = electronic_step_convergence_check_CHGCAR_conv(now_path)
+				count = 0
+				if out == 1:
+					count = 0; out_c = 1
+					while count < 3 and out_c != 0:
+						out = run_vasp(now_path,nproc,vasprun,mpi)
+						count = count+1 
+						if out == 1:  # error in vasp calculation
+							print(0)
+							sys.exit() 
+						out_c = electronic_step_convergence_check_CHGCAR_conv(now_path)
+				if count==3 and out_c == 1:
+					make_amp2_log(target,'It is not converged.')
+					print(0)
+					sys.exit() 
 			write_conv_result(now_path,enlog)
 
 	# electronic step is converged.
@@ -158,6 +184,12 @@
 	os.chdir('../')
 
 make_amp2_log(dir+'/cutoff','cut off energy test is done')
+#cp converged CHGCAR to INPUT0 
+if os.path.isfile(dir+'/cutoff/EN'+str(ENCUT-3*ENSTEP)+'/CHGCAR') and os.path.getsize(dir+'/cutoff/EN'+str(ENCUT-3*ENSTEP)+'/CHGCAR') > 1000:
+	shutil.copyfile(dir+'/cutoff/EN'+str(ENCUT-3*ENSTEP)+'/CHGCAR',dir+'/INPUT0/CHGCAR_conv')
+if  pygrep('ALGO',dir+'/cutoff/EN'+str(ENCUT-3*ENSTEP)+"/INCAR",0,0).split()[2].upper()[0] == "A":
+	wincar(dir+'/INPUT0/INCAR',dir+'/INPUT0/INCAR',["ALGO","All"],[])
+
 
 with open(enlog,'a') as result:
 	result.write("\nConvergence criterion: E/atom < "+str(ENCONV)+" eV\n")

src/dos.py

@@ -1,6 +1,6 @@
 ####################################
-# Modifier : yybbyb@snu.ac.kr      #
-# data : 2018-12-05                #
+# Date : 2020-11-05                #
+# mk01071@snu.ac.kr                #
 ####################################
 # This is for drawing density of states.
 import shutil, os, sys, subprocess, yaml
@@ -9,7 +9,7 @@
 from module_dos import *
 from input_conf import set_on_off
 from _version import __version__
-code_data = 'Version '+__version__+'. Modified at 2020-05-12'
+code_data = 'Version '+__version__+'. Modified at 2020-11-05'
 
 # Set input
 dir = sys.argv[1]
@@ -176,7 +176,7 @@
 			sys.exit() 
 		make_amp2_log(dir_dos,'CHGCAR file is generated successfully.')
 
-	wincar(dir_dos+'/INCAR',dir_dos+'/INCAR',[['NEDOS','3001'],['ISMEAR','-5'],['SIGMA','0.1']],[])
+	wincar(dir_dos+'/INCAR',dir_dos+'/INCAR',[['NEDOS','3001'],['ISMEAR','-5'],['SIGMA','0.1'],["ALGO","Normal"]],[])
 
 	incar_from_yaml(dir_dos,inp_dos['incar'])
 
@@ -189,7 +189,7 @@
 	while 1:
 		make_multiple_kpts(dir+'/kptest/kpoint.log',dir_dos+'/KPOINTS',dir_dos+'/POSCAR',inp_dos['kp_multiplier'],sym,gam_option)
 
-		wincar(dir_dos+'/INCAR',dir_dos+'/INCAR',[['NSW','0'],['ISTART','1'],['ICHARG','11'],['LCHARG','.F.']],[])
+		wincar(dir_dos+'/INCAR',dir_dos+'/INCAR',[['NSW','0'],['ICHARG','11'],['LCHARG','.F.']],[])
 		if no_rlx == 1:
 			mag_on = 2
 		else:

src/hse_gap.py

@@ -1,6 +1,7 @@
 ###########################################
-### Date: 2018-12-05			###
+### Date: 2020-11-05			###
 ### yybbyb@snu.ac.kr			###
+### mk01071@snu.ac.kr			###
 ###########################################
 # This is for estimating band gap with PBE@HSE scheme.
 import shutil, os, sys, subprocess, yaml
@@ -12,7 +13,7 @@
 from input_conf import set_on_off
 from module_relax import *
 from _version import __version__
-code_data = 'Version '+__version__+'. Modified at 2020-05-12'
+code_data = 'Version '+__version__+'. Modified at 2020-11-05'
 
 # Set input
 dir = sys.argv[1]

src/kpoint.py

@@ -1,14 +1,15 @@
 ####################################
-# date : 2018-12-06                #
+# Date: 2020-11-05                 #
 # Author : feihoon@snu.ac.kr       #
 # Modifier : yybbyb@snu.ac.kr      #
+# Modifier : mk01071@snu.ac.kr     #
 ####################################
 import os, sys, subprocess, yaml
 from module_log import *
 from module_vasprun import *
 from module_converge import *
 from _version import __version__
-code_data = 'Version '+__version__+'. Modified at 2020-05-12'
+code_data = 'Version '+__version__+'. Modified at 2020-11-05'
 
 # Set input
 dir = sys.argv[1]
@@ -98,6 +99,10 @@
             incar_for_hse(now_path+'/INCAR')
         incar_from_yaml(now_path,inp_conv['incar'])
         wincar(now_path+'/INCAR',now_path+'/INCAR',[['NSW','0'],['LCHARG','F'],['LWAVE','F']],[])
+        #if algo is all in the last step, current step uses ALGO all
+        if os.path.isfile(dir+'/kptest/KP'+str(KPL-1)+"/INCAR") and pygrep('ALGO',dir+'/kptest/KP'+str(KPL-1)+"/INCAR",0,0).split()[2].upper()[0] == "A": 
+            wincar(now_path+'/INCAR',now_path+'/INCAR',[['NSW','0'],["ALGO","All"],['LCHARG','T'],['LWAVE','F']],[])
+
         out = run_vasp(now_path,nproc,vasprun,mpi)
         if KPL == 1 or KPL == 2:
             if out == 1:  # error in vasp calculation
@@ -118,8 +123,38 @@
                     out = electronic_step_convergence_check(now_path)
 
             if out == 2:  # electronic step is not converged. (algo = normal)
-                make_amp2_log(dir+'/kptest','The calculation stops but electronic step is not converged, but pass because of too small kpoints.')
-                loopnum = 0
+#                make_amp2_log(dir+'/kptest','The calculation stops but electronic step is not converged, but pass because of too small kpoints.')
+                make_amp2_log(now_path,'We try ALGO All with a better guess on initial charge density.')
+                wincar(now_path+'/INCAR',now_path+'/INCAR',[['ALGO','All'],['NSW','0'],['LCHARG','T'],['LWAVE','F'],['AMIX','#'],['BMIX','#'],['AMIX_MAG','#'],['BMIX_MAG','#']],[])
+                if os.path.isfile(now_path+'/CHGCAR') and os.path.getsize(now_path+'/CHGCAR') > 1000:
+                    wincar(now_path+'/INCAR',now_path+'/INCAR',[['ICHARG','1']],[])
+                out = run_vasp(now_path,nproc,vasprun,mpi)
+                if out == 1: # error in vasp calculation
+                    make_amp2_log(dir+'/kptest','VASP error occurs, but pass because of too small kpoints.')
+                    out = 3
+                    loopnum = 0
+                else:
+                    out = electronic_step_convergence_check_CHGCAR_conv(now_path)
+                count = 0
+                if out == 1:
+                    count = 0; out_c = 1
+                    while count < 3 and out_c != 0:
+                        make_amp2_log(now_path,'The last CHGCAR is used as an initial guess.')
+                        out = run_vasp(now_path,nproc,vasprun,mpi)
+                        count = count+1 
+                        if out == 1:  # error in vasp calculation
+                            make_amp2_log(dir+'/kptest','VASP error occurs, but pass because of too small kpoints.')
+                            out = 3
+                            loopnum = 0
+                            break
+                        out_c = electronic_step_convergence_check_CHGCAR_conv(now_path)
+                if count==3 and out_c == 1:
+                    make_amp2_log(dir+'/kptest','The calculation stops but electronic step is not converged, but pass because of too small kpoints.')
+                    out = 3
+                    loopnum = 0
+                    continue
+                write_conv_result(now_path,kplog)
+
             elif out < 2:
                 write_conv_result(now_path,kplog)
 
@@ -137,9 +172,33 @@
                 out = electronic_step_convergence_check(now_path)
 
             if out == 2:  # electronic step is not converged. (algo = normal)
-                make_amp2_log(dir+'/kptest','The calculation stops but electronic step is not converged.')
-                print(0)
-                sys.exit()
+                make_amp2_log(now_path,'We try ALGO All with a better guess on initial charge density.')
+                wincar(now_path+'/INCAR',now_path+'/INCAR',[['ALGO','All'],['NSW','0'],['LCHARG','T'],['LWAVE','F'],['AMIX','#'],['BMIX','#'],['AMIX_MAG','#'],['BMIX_MAG','#']],[])
+                if os.path.isfile(now_path+'/CHGCAR') and os.path.getsize(now_path+'/CHGCAR') > 1000:
+                    wincar(now_path+'/INCAR',now_path+'/INCAR',[['ICHARG','1']],[])
+                out = run_vasp(now_path,nproc,vasprun,mpi)
+                if out == 1: # error in vasp calculation
+                    print(0)
+                    sys.exit()
+                else:
+                    out = electronic_step_convergence_check_CHGCAR_conv(now_path)
+                count = 0
+                if out == 1:
+                    count = 0; out_c = 1
+                    while count < 3 and out_c != 0:
+                        make_amp2_log(now_path,'The last CHGCAR is used as an initial guess.')
+                        out = run_vasp(now_path,nproc,vasprun,mpi)
+                        count = count+1 
+                        if out == 1:  # error in vasp calculation
+                            print(0)
+                            sys.exit() 
+                        out_c = electronic_step_convergence_check_CHGCAR_conv(now_path)
+                if count==3 and out_c == 1:
+                    make_amp2_log(target,'It is not converged.')
+                    print(0)
+                    sys.exit()
+                os.remove(now_path+'/CHGCAR')
+                os.remove(now_path+'/CHG') 
             # electronic step is converged.
             write_conv_result(now_path,kplog)
 
@@ -159,6 +218,8 @@
     result.write("Converged KPL: "+str(KPL-3)+'\n')
     subprocess.call(['cp',dir+'/kptest/KP'+str(KPL-3)+'/KPOINTS',dir+'/kptest/KPOINTS_converged'])
     subprocess.call(['cp',dir+'/kptest/KPOINTS_converged',dir+'/INPUT0/KPOINTS'])
+if pygrep('ALGO',dir+'/kptest/KP'+str(KPL-3)+"/INCAR",0,0).split()[2].upper()[0] == "A": 
+    wincar(dir+'/INPUT0/INCAR',dir+'/INPUT0/INCAR',[["ALGO","All"]],[])
 
 make_conv_dat(dir+'/kptest','kpoint')
 if not os.path.isfile(inp_yaml['program']['gnuplot']):