Merge pull request #125 from Chentao168/energy_qe

energy_qe

Author: amcadmus

.github/workflows/docs.yml

@@ -0,0 +1,28 @@
+# docs.yaml
+name: Auto update docs for master branch
+on:
+  push:
+    branches:
+      - master
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@master
+
+    - name: Build and Deploy
+      uses: JamesIves/github-pages-deploy-action@master
+      env:
+        ACCESS_TOKEN: ${{ secrets.BUILD_DOCS_ACCESS_TOKEN }}
+        BRANCH: gh-pages
+        FOLDER: html-site
+        BUILD_SCRIPT: |
+          apt-get install python3-pip -y &&
+          pip3 install sphinx==1.7.5 &&  
+          pip3 install sphinxcontrib-napoleon &&
+          pip3 install numpy &&  
+          pip3 install monty &&  
+          pip3 install m2r &&
+          python3 setup.py install &&  
+          cd docs && make html && mv _build/html/  ../html-site && cd  ..

dpdata/qe/scf.py

@@ -64,10 +64,11 @@ def get_coords (lines) :
     return list(atom_names), atom_numbs, atom_types, coord
 
 def get_energy (lines) :
+    energy = None
     for ii in lines :
         if '!    total energy' in ii :
-            return ry2ev * float(ii.split('=')[1].split()[0])
-    return None
+            energy = ry2ev * float(ii.split('=')[1].split()[0])
+    return energy
 
 def get_force (lines) :
     blk = get_block(lines, 'Forces acting on atoms', skip = 1)

dpdata/system.py

@@ -76,7 +76,8 @@ def __init__ (self,
                   type_map = None,
                   begin = 0,
                   step = 1,
-                  data = None) :
+                  data = None,
+                  **kwargs) :
         """
         Constructor
 
@@ -120,7 +121,7 @@ def __init__ (self,
             return
         if file_name is None :
             return
-        self.from_fmt(file_name, fmt, type_map=type_map, begin= begin, step=step)
+        self.from_fmt(file_name, fmt, type_map=type_map, begin= begin, step=step, **kwargs)
 
         if type_map is not None:
             self.apply_type_map(type_map)
@@ -1002,7 +1003,8 @@ def __init__ (self,
                   type_map = None,
                   begin = 0,
                   step = 1,
-                  data=None) :
+                  data=None,
+                  **kwargs) :
         """
         Constructor
 
@@ -1045,7 +1047,7 @@ def __init__ (self,
            return
         if file_name is None :
             return
-        self.from_fmt(file_name, fmt, type_map=type_map, begin= begin, step=step)
+        self.from_fmt(file_name, fmt, type_map=type_map, begin= begin, step=step, **kwargs)
         if type_map is not None:
             self.apply_type_map(type_map)
 

setup.py

@@ -37,7 +37,8 @@
               'dpdata/pwmat', 
               'dpdata/amber',
               'dpdata/fhi_aims',
-              'dpdata/gromacs'],
+              'dpdata/gromacs'
+    ],
     package_data={'dpdata':['*.json']},
     classifiers=[
         "Programming Language :: Python :: 3.6",

tests/qe.scf/Al.in

@@ -0,0 +1,43 @@
+&CONTROL
+  calculation      = "scf",
+  pseudo_dir       = "../",
+  prefix           = "Aluminium",
+  wf_collect       = .True.,
+  tstress          = .True.,
+  tprnfor          = .True.,
+  outdir           = "./",
+  iprint           = 1,
+/
+&SYSTEM
+  ibrav            = 0,
+  nat              = 4,
+  ntyp             = 1,
+  occupations      ='smearing',
+  smearing         ='fermi-dirac',
+  degauss          = 0.001d0,
+  nosym            = .true.,
+  ecutwfc          = 50,
+  nbnd             = 12,
+/
+&ELECTRONS
+  electron_maxstep = 200,
+  mixing_mode      = 'plain',
+  conv_thr         = 1.0D-8,
+  mixing_beta      = 0.7D0,
+/
+CELL_PARAMETERS (angstrom)
+4.04 0 0
+0 4.04 0
+0 0 4.04
+
+ATOMIC_SPECIES
+Al  26.98 Al.pbe-n-nc.UPF
+
+ATOMIC_POSITIONS (crystal)
+Al 0 0 0
+Al 0 0.5 0.5
+Al 0.5 0 0.5
+Al 0.5 0.5 0
+
+K_POINTS (automatic)
+2 2 2 0 0 0