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dimonaks · Dec 6, 2016 · d846a9e · d846a9e
1 parent 78dcbc1
commit d846a9e
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Showing 6 changed files with 223 additions and 70 deletions.
diff --git a/calc_manage.py b/calc_manage.py
@@ -818,7 +818,9 @@ def add_loop(it, setlist, verlist, calc = None, conv = None, varset = None,
         if it_folder == None:
             print_and_log('Error! Please provide local folder for new ', it, 'structure using *it_folder* argument! ', imp = 'Y')
 
-        mat_proj_st_id, input_geo_file = get_structure_from_matproj(struct_des, it, it_folder, verlist[0], mat_proj_cell, mat_proj_id)
+        st = get_structure_from_matproj(it, it_folder, verlist[0], mat_proj_cell, mat_proj_id)
+        mat_proj_st_id = st.mat_proj_st_id
+        input_geo_file = st.input_geo_file
         input_geo_format = 'vasp'
 
     elif input_geo_format == 'cee_database':
@@ -3107,7 +3109,7 @@ def get_structure_from_cee_database(it, it_folder, ver, cee_struct_type = 'exp',
 
 
 
-def get_structure_from_matproj(struct_des, it, it_folder, ver, mat_proj_cell = None, mat_proj_id = None):
+def get_structure_from_matproj(it = None, it_folder = None, ver = None, mat_proj_cell = '', mat_proj_id = None):
     """
     Take structures from Mat. projects
 
@@ -3166,14 +3168,24 @@ def get_structure_from_matproj(struct_des, it, it_folder, ver, mat_proj_cell = N
         # print(st_pmg.lattice)
         # sys.exit()
 
+    if it:
+        add_des(header.struct_des, it, it_folder, des = 'taken automatically from materialsproject.org: '+groundstate_st_id,)
+        path2poscar = it_folder+'/'+it+'/'+groundstate_st_id+".POSCAR-"+str(ver)
+        makedir(path2poscar)
+    else:
+        path2poscar = groundstate_st_id+".POSCAR"
 
-    add_des(struct_des, it, it_folder, des = 'taken automatically from materialsproject.org: '+groundstate_st_id,)
-    path2poscar = it_folder+'/'+it+'/'+groundstate_st_id+".POSCAR-"+str(ver)
-    makedir(path2poscar)
-    Poscar(st_pmg).write_file(path2poscar, direct=True, vasp4_compatible=True, )
-    print_and_log("File "+path2poscar+" was written\n")
 
-    return groundstate_st_id, path2poscar
+    Poscar(st_pmg).write_file(path2poscar, direct=True, vasp4_compatible=True, )
+    print_and_log('Structure', groundstate_st_id, 'downloaded from materialsproject.org\n',
+        'File '+path2poscar+" was written", imp = 'y')
+
+    st = smart_structure_read(input_geo_file = path2poscar)
+    st.groundstate_st_id = groundstate_st_id
+    st.input_geo_file    = path2poscar
+
+
+    return st
 
     #pymatgen drafts, can be useful
 

diff --git a/classes.py b/classes.py
@@ -33,7 +33,7 @@
 from small_functions import cat_files, grep_file
 from functions import (read_vectors, read_list, words, local_surrounding, 
     xred2xcart, xcart2xred, element_name_inv, calculate_voronoi,
-    get_from_server, push_to_server, run_on_server, list2string, makedir, write_xyz)
+    get_from_server, push_to_server, run_on_server, list2string, makedir, write_xyz, write_lammps)
 
 
 
@@ -336,8 +336,10 @@ def write_cif(self, filename):
 
     def write_xyz(self, *args, **kwargs):
         #see description for write_xyz()
-        return write_xyz(*args, **kwargs)
+        return write_xyz(self, *args, **kwargs)
 
+    def write_lammps(self, *args, **kwargs):
+        return write_lammps(self, *args, **kwargs)
 
 
 

diff --git a/functions.py b/functions.py
@@ -177,9 +177,11 @@ def makedir(path):
     *path* - path to some file 
     Make dirname(path) directory if it does not exist
     """
-    if not os.path.exists(os.path.dirname(path)):
-        os.makedirs(os.path.dirname(path))
-        print_and_log("Directory "+os.path.dirname(path)+" was created\n")
+    dirname = os.path.dirname(path)
+
+    if dirname and not os.path.exists(dirname):
+        os.makedirs(dirname)
+        print_and_log("Directory", dirname, " was created", imp = 'y')
     return
 
 
@@ -931,13 +933,12 @@ def update_var():
     return
 
 
-def write_lammps(cl, state, filepath = ''):
-    """Writes structure in lammps format """
-    if state == 'end':
-        st = cl.end
-    elif state == 'init':
-        st = cl.init
-
+def write_lammps(st, filename = '', charges = None):
+    """Writes structure in lammps format 
+
+    charges (list of float) - list of charges for each atom type
+    """
+
     rprimd = st.rprimd
     xcart  = st.xcart
     xred   = st.xred
@@ -948,76 +949,94 @@ def write_lammps(cl, state, filepath = ''):
     natom = st.natom
 
     if natom != len(xred) != len(xcart) != len(typat) or len(znucl) != max(typat): 
-        print_and_log( "Error! write_xyz: check your arrays.\n\n"    )
+        print_and_log( "Error! write_xyz: check your structure"    )
 
-    if name == '': name = 'noname'
+    if name == '': 
+        name = 'noname'
     if xcart == [] or len(xcart) != len(xred):
         print_and_log( "Warining! write_xyz: len(xcart) != len(xred) making xcart from xred.\n", imp = 'y')
         xcart = xred2xcart(xred, rprimd)
         #print xcart[1]
 
-    if not filepath:
-        filepath = 'lammps/'+name+".lammps"
-    if not os.path.exists(os.path.dirname(filepath)):
-        os.makedirs(os.path.dirname(filepath))
+    if not filename:
+        filename = 'lammps/'+name
+
+    filename+='.inp'
+
+    makedir(filename)
+
+
 
     """Write lammps structure file;  """
-    if 0:
+    if 1:
         """ My version; valid only for octahedral cells""" 
-        with open(filepath+'','w') as f:
+        printlog( "Warining! write_lammps(): this func supports only orthogonal cells", imp = 'Y')
+
+        with open(filename+'','w') as f:
             f.write("Lammps format "+name+'\n')
             f.write(str(natom)+" atoms\n")
             f.write(str(ntypat)+" atom types\n")
-            f.write("0 "+str(rprimd[0][0])+" xlo xhi\n")
-            f.write("0 "+str(rprimd[1][1])+" ylo yhi\n")
-            f.write("0 "+str(rprimd[2][2])+" zlo zhi\n")
-            f.write("0.000000    0.000000    0.000000   xy xz yz\n")
+            f.write("{:10.8f}  {:10.8f}  xlo xhi\n".format(0, rprimd[0][0]))
+            f.write("{:10.8f}  {:10.8f}  ylo yhi\n".format(0, rprimd[1][1]))
+            f.write("{:10.8f}  {:10.8f}  zlo zhi\n".format(0, rprimd[2][2]))
+            f.write("0.00000000  0.00000000  0.00000000  xy xz yz\n")
             f.write("\nAtoms\n\n")
 
             for i, x in enumerate(xcart):
-                f.write("{0:d} {1:d} {2:f} {3:f} {4:f}\n".format(i+1, typat[i], x[0], x[1], x[2] ))
+                f.write("{0:8d} {1:2d}".format(i+1, typat[i]))
+                if charges:
+                    f.write(" {:6.3f}".format(charges[typat[i]-1] ) )
+                f.write(" {:12.6f}  {:12.6f}  {:12.6f}\n".format(x[0], x[1], x[2] ))
+
+
+
             f.write("\n")
+
+        printlog('File', filename, 'was written', imp = 'y')
+
+
+
     else:
         """Write poscar and convert from poscar to lammps using external script; Valid for arbitary cells"""
         cl.write_structure('POSCAR', 'dir', path = 'voronoi_analysis/', state = state)
         runBash("voronoi_analysis/VASP-poscar2lammps.awk voronoi_analysis/POSCAR > "+filepath)
 
 
 
-
-    """Write lammps.in file """
-    with open('voronoi_analysis/voronoi.in','w') as f:
-        f.write("""units           metal
-                atom_style atomic
-                boundary        p p p\n""")
-        f.write("read_data   /home/aksenov/programs/Simulation_wrapper/siman1/voronoi_analysis/structure.lammps\n")
-#         f.write('lattice   custom 1 ')
-#         for i, a in enumerate(rprimd):
-#             f.write(' a'+str(i+1))
-#             for x in a:
-#                 f.write(' '+str(x))
-
-#         f.write(' &\n')
-#         for x in xred:
-#             f.write(' basis {0:f} {1:f} {2:f}&\n '.format(x[0], x[1], x[2]) )
-#         f.write("""\n
-# region 1 prism 0 1 0 1 0 1  1 0 0
-# create_box 1 prism
-# create_atoms 1 prism""")
-
-        for i in range(ntypat):
-            f.write('\nmass '+str(i+1)+' '+str(int(znucl[i]))+'\n')
-
-        f.write('pair_style      lj/cut 2.0\n')
-        for i in range(ntypat):
-            for j in range(i, ntypat):
-                f.write('pair_coeff      '+str(i+1)+' '+str(j+1)+' 0.0 1.0\n')
+    if 0:
+        """Write lammps.in file """
+        with open('voronoi_analysis/voronoi.in','w') as f:
+            f.write("""units           metal
+                    atom_style atomic
+                    boundary        p p p\n""")
+            f.write("read_data   /home/aksenov/programs/Simulation_wrapper/siman1/voronoi_analysis/structure.lammps\n")
+    #         f.write('lattice   custom 1 ')
+    #         for i, a in enumerate(rprimd):
+    #             f.write(' a'+str(i+1))
+    #             for x in a:
+    #                 f.write(' '+str(x))
+            
+    #         f.write(' &\n')
+    #         for x in xred:
+    #             f.write(' basis {0:f} {1:f} {2:f}&\n '.format(x[0], x[1], x[2]) )
+    #         f.write("""\n
+    # region 1 prism 0 1 0 1 0 1  1 0 0
+    # create_box 1 prism
+    # create_atoms 1 prism""")
+
+            for i in range(ntypat):
+                f.write('\nmass '+str(i+1)+' '+str(int(znucl[i]))+'\n')
+            
+            f.write('pair_style      lj/cut 2.0\n')
+            for i in range(ntypat):
+                for j in range(i, ntypat):
+                    f.write('pair_coeff      '+str(i+1)+' '+str(j+1)+' 0.0 1.0\n')
 
 
-        f.write("""compute v1 all voronoi/atom
-                dump    d1 all custom 1 /home/aksenov/programs/Simulation_wrapper/siman1/voronoi_analysis/dump.voro id type x y z c_v1[1] c_v1[2]
-                run 0
-                uncompute v1\n""")
+            f.write("""compute v1 all voronoi/atom
+                    dump    d1 all custom 1 /home/aksenov/programs/Simulation_wrapper/siman1/voronoi_analysis/dump.voro id type x y z c_v1[1] c_v1[2]
+                    run 0
+                    uncompute v1\n""")
 
     return
 

diff --git a/geo.py b/geo.py
@@ -164,4 +164,6 @@ def determine_symmetry_positions(st, element):
         if el in element:
             positions[pos].append(i)
 
+
+    printlog('I found ', len(positions), 'non-eqiu')
     print(positions)
diff --git a/tutorials/mp-7000.POSCAR b/tutorials/mp-7000.POSCAR
@@ -0,0 +1,16 @@
+Si3 O6
+1.0
+5.021502 0.000000 0.000000
+-2.510751 4.348749 0.000000
+0.000000 0.000000 5.510570
+6 3
+direct
+0.256094 0.414854 0.794543 O
+0.585146 0.841240 0.127877 O
+0.158760 0.743906 0.461210 O
+0.414854 0.256094 0.205457 O
+0.743906 0.158760 0.538790 O
+0.841240 0.585146 0.872123 O
+0.523695 0.523695 0.000000 Si
+0.000000 0.476305 0.666667 Si
+0.476305 0.000000 0.333333 Si