add XTB1 to the DFTB+ module

bin/cmmde.py

@@ -357,7 +357,7 @@ if opt.job == 'checkopt' and opt.software == 'dock':
     checkopt(opt.nligands)
 
 if opt.software == 'dftb':
-    if '.xyz' in opt.input:
+    if '.xyz' in opt.input or '.gen' in opt.input:
         geom = opt.input
     elif 'POSCAR' in opt.input or '.poscar' in opt.input:
         poscar2gen(opt.input)

lib/cmmde_dftb.py

@@ -225,18 +225,19 @@ def dftb(geom,job,activeatoms,method,parapath,dispersion,kpts,hcorr):
       0 0 {}
       {} {} {}
    }}
-        		}}""".format(kpts[0],kpts[1],kpts[2],shift,shift,shift))
-        print("Hamiltonian = DFTB {",file=f)
-        if method == 'DFTB2':
-            print("scc = Yes",file=f)
-            print("MaxSCCIterations = 1000",file=f)
-        if method == 'DFTB3diag':
-            print("""scc = Yes
+        		}}""".format(kpts[0],kpts[1],kpts[2],shift,shift,shift),file=f)
+        else:
+        	print("Hamiltonian = DFTB {",file=f)
+        	if method == 'DFTB2':
+        		print("scc = Yes",file=f)
+        		print("MaxSCCIterations = 1000",file=f)
+        		if method == 'DFTB3diag':
+        			print("""scc = Yes
     ThirdOrder = Yes
     MaxSCCIterations = 1000
 """,file=f)
-        if method == 'DFTB3':
-            print("""scc = Yes
+        	if method == 'DFTB3':
+        		print("""scc = Yes
     ThirdOrderFull = Yes
               """,file=f)
         ## Koreksi ikatan hidrogen
@@ -246,13 +247,13 @@ def dftb(geom,job,activeatoms,method,parapath,dispersion,kpts,hcorr):
            'DFTB2': '4.5'
         }
         if hcorr == 'hdamp':
-            print("""HCorrection = Damping {{
+        	print("""HCorrection = Damping {{
  Exponent = {}
 }}""".format(hdamp[method]),file=f)
-        if hcorr == 'H5':
-            print("""HCorrection = H5{ }""",file=f)
-        if dispersion == 'D3':
-            print("""Dispersion = DftD3 {
+        	if hcorr == 'H5':
+        		print("""HCorrection = H5{ }""",file=f)
+        	if dispersion == 'D3':
+        		print("""Dispersion = DftD3 {
     Damping = ZeroDamping {
         sr6 = 0.7461
         alpha6 = 14.0
@@ -260,8 +261,8 @@ def dftb(geom,job,activeatoms,method,parapath,dispersion,kpts,hcorr):
     s6 = 1.0
     s8 = 3.209
 }""",file=f)
-        if dispersion == 'D3BJ':
-            print("""Dispersion = DftD3 {
+        	if dispersion == 'D3BJ':
+        		print("""Dispersion = DftD3 {
     Damping = BeckeJohnson {
         a1 = 0.5719
         a2 = 3.6017
@@ -269,8 +270,8 @@ def dftb(geom,job,activeatoms,method,parapath,dispersion,kpts,hcorr):
     s6 = 1.0
     s8 = 0.5883
         }""",file=f)
-        if dispersion == 'D3H5':
-            print("""Dispersion = DftD3{
+        	if dispersion == 'D3H5':
+        		print("""Dispersion = DftD3{
     Damping = ZeroDamping{
      sr6 = 1.25
      alpha6 = 29.61
@@ -279,41 +280,41 @@ def dftb(geom,job,activeatoms,method,parapath,dispersion,kpts,hcorr):
      s8 = 0.49
      HHRepulsion = Yes
 }""",file=f)
-        print("""SlaterKosterFiles = Type2FileNames {{
+        	print("""SlaterKosterFiles = Type2FileNames {{
         Prefix = {}/
         Separator = "-"
         Suffix = ".skf" """.format(parapath),file=f)
-        print('}',file=f)
+        	print('}',file=f)
     # Mapping bilangan kuantum azimuth ke penamaan orbital
-        azi2orb = {'1':'s','2':'p','3':'d','4':'f'}
+        	azi2orb = {'1':'s','2':'p','3':'d','4':'f'}
 
-        print("MaxAngularMomentum {",file=f)
-        for element in elements:
-            print("""{} = "{}" """.format(element,azi2orb[azimuth(element)]),file=f)
-        print("}",file=f)
+        	print("MaxAngularMomentum {",file=f)
+        	for element in elements:
+        		print("""{} = "{}" """.format(element,azi2orb[azimuth(element)]),file=f)
+        	print("}",file=f)
 
-        if method == 'DFTB3':
-            print("HubbardDerivs {",file=f)
-            for element in elements:
-                print("""{} = {}""".format(element,hubbard(element)),file=f)
-            print("}",file=f)
+        	if method == 'DFTB3':
+        		print("HubbardDerivs {",file=f)
+        		for element in elements:
+        			print("""{} = {}""".format(element,hubbard(element)),file=f)
+        		print("}",file=f)
     # Informasi K-points
-        kpts = kpts.split('x')
-        shift = 0
-        if int(kpts[0])%2 == 0:
-            shift+=0.5
-        else:
-            shift +=0
+        	kpts = kpts.split('x')
+        	shift = 0
+        	if int(kpts[0])%2 == 0:
+        		shift+=0.5
+        	else:
+        		shift +=0
         # if 'F' or 'S' in coord_type:
-        if '.gen' in geom:
-            print("""KPointsAndWeights = SuperCellFolding {{
-                {} 0 0
-                0 {} 0
-                0 0 {}
-                {} {} {}
-            }}""".format(kpts[0],kpts[1],kpts[2],shift,shift,shift),file=f)
+        	if '.gen' in geom:
+        		print("""KPointsAndWeights = SuperCellFolding {{
+                	{} 0 0
+                	0 {} 0
+                	0 0 {}
+                	{} {} {}
+            	}}""".format(kpts[0],kpts[1],kpts[2],shift,shift,shift),file=f)
 
-        print("}", file=f)
+        	print("}", file=f)
         if job == 'dos':
             print("Analysis {",file=f)
             print("   ProjectStates {",file=f)