new method for assigning potcar

deepmodeling · Jun 28, 2018 · 8a78d09 · 8a78d09
1 parent e1b9172
commit 8a78d09
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Showing 2 changed files with 22 additions and 3 deletions.
diff --git a/data/gen.py b/data/gen.py
@@ -211,6 +211,7 @@ def place_element (jdata) :
 
 def make_vasp_relax (jdata) :
     out_dir = jdata['out_dir']
+    potcars = jdata['potcars']
     encut = jdata['encut']
     kspacing = jdata['kspacing']
     kgamma = jdata['kgamma']
@@ -226,7 +227,11 @@ def make_vasp_relax (jdata) :
         os.remove(os.path.join(work_dir, 'POTCAR'))
     shutil.copy2(os.path.join(vasp_dir, 'INCAR.rlx' ), 
                  os.path.join(work_dir, 'INCAR'))
-    shutil.copy2(os.path.join(vasp_dir, 'POTCAR'), work_dir)
+    out_potcar = os.path.join(work_dir, 'POTCAR')
+    with open(out_potcar, 'w') as outfile:
+        for fname in potcars:
+            with open(fname) as infile:
+                outfile.write(infile.read())
 
     os.chdir(work_dir)
     replace('INCAR', 'ENCUT=.*', 'ENCUT=%f' % encut)
@@ -250,6 +255,7 @@ def make_vasp_relax (jdata) :
 def make_scale(jdata):
     out_dir = jdata['out_dir']
     scale = jdata['scale']    
+    skip_relax = jdata['skip_relax']    
 
     cwd = os.getcwd()
     init_path = os.path.join(out_dir, global_dirname_02)
@@ -265,7 +271,11 @@ def make_scale(jdata):
         for jj in scale :
             pos_src = os.path.join(os.path.join(init_path, ii), 'CONTCAR')
             if not os.path.isfile(pos_src):
-                raise RuntimeError("not file %s, vasp relaxation should be run before scale poscar")
+                if skip_relax :
+                    pos_src = os.path.join(os.path.join(init_path, ii), 'POSCAR')
+                    assert(os.path.isfile(pos_src))
+                else :
+                    raise RuntimeError("not file %s, vasp relaxation should be run before scale poscar")
             scale_path = os.path.join(work_path, ii)
             scale_path = os.path.join(scale_path, "sys-%.3f" % jj)
             create_path(scale_path)
@@ -317,6 +327,7 @@ def pert_scaled(jdata) :
 
 def make_vasp_md(jdata) :
     out_dir = jdata['out_dir']
+    potcars = jdata['potcars']
     scale = jdata['scale']    
     encut = jdata['encut']
     kspacing = jdata['kspacing']
@@ -340,7 +351,11 @@ def make_vasp_md(jdata) :
     create_path(path_md)
     shutil.copy2(os.path.join(vasp_dir, 'INCAR.md'), 
                  os.path.join(path_md, 'INCAR'))
-    shutil.copy2(os.path.join(vasp_dir, 'POTCAR'), path_md)
+    out_potcar = os.path.join(path_md, 'POTCAR')
+    with open(out_potcar, 'w') as outfile:
+        for fname in potcars:
+            with open(fname) as infile:
+                outfile.write(infile.read())
     os.chdir(path_md)
     replace('INCAR', 'ENCUT=.*', 'ENCUT=%f' % encut)
     replace('INCAR', 'ISIF=.*', 'ISIF=2')

diff --git a/data/param.json b/data/param.json
@@ -3,10 +3,14 @@
     "latt":		4.03,
     "super_cell":	[2, 1, 1],
     "elements":		["Al", "Mg"],
+    "potcars":		["/home/wanghan/Soft/vasp/potcar.54/potpaw_PBE.54/Al/POTCAR",
+			 "/home/wanghan/Soft/vasp/potcar.54/potpaw_PBE.54/Mg/POTCAR"
+			],
     "encut":		600,
     "kspacing":		0.06,
     "kgamma":		false,
     "scale":		[0.96, 0.98, 1.00, 1.02, 1.04, 1.06],
+    "skip_relax":	false,
     "pert_numb":	100,
     "pert_box":		0.03,
     "pert_atom":	0.01,