Merge devel into master (#395)

Author: amcadmus

README.md

@@ -80,6 +80,7 @@ The `System` or `LabeledSystem` can be constructed from the following file forma
 | Amber   | multi       | True         | True    | LabeledSystem | 'amber/md'           |
 | Amber/sqm | sqm.out   | False        | False   | System        | 'sqm/out'            |
 | Gromacs | gro         | True         | False   | System        | 'gromacs/gro'        |
+| ABACUS  | STRU        | False        | False   | System        | 'abacus/stru'         |
 | ABACUS  | STRU        | False        | True    | LabeledSystem | 'abacus/scf'         |
 | ABACUS  | cif         | True         | True    | LabeledSystem | 'abacus/md'          |
 | ABACUS  | STRU        | True         | True    | LabeledSystem | 'abacus/relax'       |

dpdata/abacus/scf.py

@@ -59,21 +59,15 @@ def get_cell(geometry_inlines):
     cell = celldm*np.array(cell)
     return celldm, cell
 
-def get_coords(celldm, cell, geometry_inlines, inlines):
+def get_coords(celldm, cell, geometry_inlines, inlines=None):
     coords_lines = get_block(geometry_inlines, "ATOMIC_POSITIONS", skip=0)
     # assuming that ATOMIC_POSITIONS is at the bottom of the STRU file
     coord_type = coords_lines[0].split()[0].lower() # cartisan or direct
     atom_names = [] # element abbr in periodic table 
     atom_types = [] # index of atom_names of each atom in the geometry
     atom_numbs = [] # of atoms for each element
     coords = [] # coordinations of atoms
-    ntype = 0
-    for line in inlines:
-        if "ntype" in line and "ntype"==line.split()[0]:
-            ntype = int(line.split()[1])
-            break
-    if ntype <= 0:
-        raise RuntimeError('ntype cannot be found in INPUT file.')
+    ntype = get_nele_from_stru(geometry_inlines)
     line_idx = 1 # starting line of first element
     for it in range(ntype):
         atom_names.append(coords_lines[line_idx].split()[0])

tests/abacus.md.nostress/INPUT

@@ -1,8 +1,7 @@
 INPUT_PARAMETERS
 #Parameters	(General)
 suffix          autotest
-pseudo_dir		./
-ntype			1	
+pseudo_dir		./	
 nbands			8
 calculation     md
 

tests/abacus.md.unconv/INPUT

@@ -1,6 +1,5 @@
 INPUT_PARAMETERS
 calculation 	md
-ntype 		2
 nbands 		8
 
 ecutwfc 	50.000000

tests/abacus.md/INPUT

@@ -2,7 +2,6 @@ INPUT_PARAMETERS
 #Parameters (1.General)
 suffix                  abacus
 calculation             md
-ntype                   2
 nbands                  6
 symmetry                0
 

tests/abacus.relax/INPUT

@@ -2,7 +2,6 @@ INPUT_PARAMETERS
 #Parameters (1.General)
 suffix                  abacus
 calculation             cell-relax
-ntype                   2
 nbands                  6
 symmetry                1
 

tests/abacus.scf/INPUT.fail

@@ -4,7 +4,6 @@ suffix 			ch4fail
 stru_file 	        STRU.ch4 #the filename of file containing atom positions
 kpoint_file        	KPT.ch4 #the name of file containing k points
 pseudo_dir		./
-ntype			2
 nbands		  	8
 #Parameters (Accuracy)
 ecutwfc			100

tests/abacus.scf/INPUT.ok

@@ -4,7 +4,6 @@ suffix 			ch4
 stru_file 	        STRU.ch4 #the filename of file containing atom positions
 kpoint_file        	KPT.ch4 #the name of file containing k points
 pseudo_dir		./
-ntype			2
 nbands		  	8
 #Parameters (Accuracy)
 ecutwfc			100