Merge branch ''Geom_view'' into 'develop'

'geom view'

See merge request west-devel/westpy!3

debug_Geometry_view_addFracCoordAtom.ipynb

+%% Cell type:code id: tags:
+
+``` python
+from westpy import *
+
+def xyz2center(in_xyz,out_xyz,box_length=30):
+    '''
+    in_xyz: input xyz file in unit A
+    out_xyz: output xyz file where coords are centered in simulation box.
+    box_length:  in unit Bohr
+    '''
+    from westpy.units import Angstrom
+    import pandas as pd
+    BOHR2A = 1.0 / Angstrom
+    #convert box length 2 A:
+    box_length *= BOHR2A
+    #read in_xyz in unit A
+    dict_atoms = {'element':[], 'x':[], 'y':[], 'z':[]}
+    with open(in_xyz,'r') as f:
+        n_atoms=int(f.readline())
+        f.readline()
+        for _ in range(n_atoms):
+            element, x, y, z = f.readline().split()
+            dict_atoms['element'].append(element.strip())
+            dict_atoms['x'].append(float(x))
+            dict_atoms['y'].append(float(y))
+            dict_atoms['z'].append(float(z))
+        assert(len(dict_atoms['x']) == n_atoms)
+    df_atoms_centered=pd.DataFrame(dict_atoms)
+    # shift in_xyz coords by [box_length/2,box_length/2,box_length/2]
+    df_atoms_centered[['x','y','z']] -= df_atoms_centered[['x','y','z']].mean(axis=0)
+    df_atoms_centered[['x','y','z']] += box_length/2.0
+    # save to out_xyz
+    xyz=str(len(df_atoms_centered))+'\n\n'
+    for row in df_atoms_centered.values:
+        xyz += " ".join([str(e) for e in row]) + '\n'
+    with open(out_xyz,'w') as f:
+        f.write(xyz)
+```
+
+%%%% Output: stream
+
+    The autoreload extension is already loaded. To reload it, use:
+      %reload_ext autoreload
+    
+     _    _ _____ _____ _____
+    | |  | |  ___/  ___|_   _|
+    | |  | | |__ \ `--.  | |_ __  _   _
+    | |/\| |  __| `--. \ | | '_ \| | | |
+    \  /\  / |___/\__/ / | | |_) | |_| |
+     \/  \/\____/\____/  \_/ .__/ \__, |
+                           | |     __/ |
+                           |_|    |___/
+    
+    WEST version     :  4.1.0
+    Today            :  2020-06-29 22:33:03.328128
+
+%% Cell type:markdown id: tags:
+
+# Geometry.view()  Si35H36
+
+%% Cell type:code id: tags:
+
+``` python
+#download xyz
+url = 'https://journals.aps.org/prx/supplemental/10.1103/PhysRevX.6.041002/si35h36.xyz'
+fname = 'si35h36.xyz'
+download(url=url, fname='si35h36.xyz')
+#center it to fit geom.setCell((box_length,0,0),(0,box_length,0),(0,0,box_length))
+box_length = 30 #Bohr
+center2box_fname = 'centered_si35h36.xyz'
+xyz2center(in_xyz=fname,out_xyz=center2box_fname,box_length=box_length)
+#creat geom
+geom = Geometry()
+geom.setCell((box_length,0,0),(0,box_length,0),(0,0,box_length))
+geom.addAtomsFromXYZFile(center2box_fname)
+geom.addSpecies( "Si", "http://www.quantum-simulation.org/potentials/sg15_oncv/upf/Si_ONCV_PBE-1.2.upf")
+geom.addSpecies( "H", "http://www.quantum-simulation.org/potentials/sg15_oncv/upf/H_ONCV_PBE-1.2.upf")
+geom.view()
+```
+
+%%%% Output: stream
+
+    Downloaded file:  si35h36.xyz , from url:  https://journals.aps.org/prx/supplemental/10.1103/PhysRevX.6.041002/si35h36.xyz
+
+%%%% Output: display_data
+
+
+%% Cell type:code id: tags:
+
+``` python
+geom.view(style='line')
+```
+
+%%%% Output: display_data
+
+
+%% Cell type:code id: tags:
+
+``` python
+geom.view(style='sphere')
+```
+
+%%%% Output: display_data
+
+
+%% Cell type:code id: tags:
+
+``` python
+geom.view(ix=2,iy=2,iz=1)
+```
+
+%%%% Output: display_data
+
+
+%% Cell type:markdown id: tags:
+
+# Geometry.view()  HBN
+
+%% Cell type:code id: tags:
+
+``` python
+from westpy.units import Angstrom
+import numpy as np
+A2BOHR = Angstrom
+```
+
+%% Cell type:code id: tags:
+
+``` python
+geom = Geometry()
+#define unit cell
+#>>    ibrav = 4           ,
+#>>    celldm(1) = 4.695926777902829 ,
+#>>    celldm(3) = 8.048362859199854 ,
+# 4     Hexagonal and Trigonal P   celldm(3)=c/a
+#       v1 = a(1,0,0),  v2 = a(-1/2,sqrt(3)/2,0),  v3 = a(0,0,c/a)
+#https://materialsproject.org/materials/mp-984/
+celldm_1 = 2.51242804*A2BOHR         #bohr
+celldm_3 = 7.70726501/2.0/2.512      #c/a
+geom.addSpecies( "B", "http://www.quantum-simulation.org/potentials/sg15_oncv/upf/B_ONCV_PBE-1.2.upf")
+geom.addSpecies( "N", "http://www.quantum-simulation.org/potentials/sg15_oncv/upf/N_ONCV_PBE-1.2.upf")
+geom.setCell(a1=(1,0,0), a2=(-1/2,np.sqrt(3)/2,0), a3=(0,0,celldm_3), units=celldm_1)
+geom.addFracCoordAtom('B', (1.0/3,2.0/3,0.5) )
+geom.addFracCoordAtom('N', (2.0/3,1.0/3,0.5) )
+```
+
+%% Cell type:code id: tags:
+
+``` python
+geom.view(style='stick')
+```
+
+%%%% Output: display_data
+
+
+%% Cell type:code id: tags:
+
+``` python
+geom.view(style='line',ix=5,iy=5,iz=2)
+```
+
+%%%% Output: display_data
+
+
+%% Cell type:code id: tags:
+
+``` python
+geom.view(style='sphere',ix=2,iy=2,iz=1,width=400,height=400)
+```
+
+%%%% Output: display_data
+
+
+%% Cell type:code id: tags:
+
+``` python
+```

setup.py

@@ -27,7 +27,8 @@ setup(name='westpy',
           'urllib3', 
           'prompt-toolkit',
           'sphinx', 
-          'sphinx_rtd_theme'
+          'sphinx_rtd_theme',
+          'py3Dmol'
       ],
       python_requires='>=2.7, >=3.0, !=3.0.*, !=3.1.*, !=3.2.*, <4',
       zip_safe=True)

westpy/geometry.py

@@ -150,18 +150,46 @@ class Geometry(object) :
       self.atoms.append( Atom(symbol, position, units) )
       self.isSet["atoms"] = True
    #
-   def __addAtomsFromXYZLines(self, lines ) : 
+   def addFracCoordAtom(self, symbol, frac_coord):
+      """adds a single atom by fractional coords
+      :param symbol: chemical symbol
+      :type symbol: string
+      :param position: position
+      :type position: 3-dim tuple
+
+      :Example:
+
+      >>> from westpy import *
+      >>> geom = Geometry()
+      >>> geom.addFracCoordAtom( "Si", (0,1/3.0,2/3.0) )
+      """
+      if not self.isSet["cell"]:
+         print('Set cell first!')
+         return
+      import numpy as np
+      from westpy import Atom, Bohr
+      M = np.matrix([self.cell['a1'], self.cell['a2'], self.cell['a3']]).tolist()
+      self.atoms.append(Atom(symbol, tuple(np.array(frac_coord)@M), units=Bohr))
+      self.isSet["atoms"] = True
+
+
+   def __addAtomsFromXYZLines(self, lines, decode=True ) :
       """Adds atoms from XYZ lines.
    
       :param lines: lines read from XYZ file (only one image)
       :type lines: list of string
+      :param decode:
+      :type bool:
       """
       #
       from westpy import Angstrom 
       natoms = int(lines[0])
       for line in lines[2:2+natoms] : 
          symbol, x, y, z = line.split()[:4]
-         self.addAtom( symbol.decode("utf-8"), (float(x), float(y), float(z)), units=Angstrom )
+         if decode:
+            self.addAtom( symbol.decode("utf-8"), (float(x), float(y), float(z)), units=Angstrom )
+         else:
+            self.addAtom( symbol, (float(x), float(y), float(z)), units=Angstrom )
    #
    def addAtomsFromXYZFile(self, fname ) : 
       """Adds atoms from XYZ file (only one image).
@@ -178,7 +206,7 @@ class Geometry(object) :
       # 
       with open(fname,'r') as file: 
          lines = file.readlines()
-      self.__addAtomsFromXYZLines(lines) 
+      self.__addAtomsFromXYZLines(lines,  decode=False)
    #
    def addAtomsFromOnlineXYZ(self, url ) : 
       """Adds atoms from XYZ file (only one image) located at url.
@@ -196,7 +224,7 @@ class Geometry(object) :
       import urllib.request
       with urllib.request.urlopen(url) as response :
          lines = response.readlines()
-      self.__addAtomsFromXYZLines(lines)
+      self.__addAtomsFromXYZLines(lines,  decode=True)
    #
    def getNumberOfAtoms(self) : 
       """Returns number of atoms.
@@ -294,3 +322,63 @@ class Geometry(object) :
       from westpy import download 
       for key in self.species.keys() :
          download( self.species[key]["url"], fname=self.species[key]["fname"] )
+
+   def view(self,  style='stick',width=800,height=800, ix=1, iy=1, iz=1, debug=False):
+      """Display simulation box geom in Angstrom.
+      ix, iy, iz is the perodic display to system
+      style can be line, stick, sphere.
+
+      :param style:
+      :param width:
+      :param height:
+      :param ix:
+      :param iy:
+      :param iz:
+      :param debug:
+      :return:
+      """
+      import py3Dmol
+      import numpy as np
+      from westpy.units import Angstrom
+      BOHR2A = 1.0 / Angstrom
+      a1 = self.cell["a1"] * BOHR2A
+      a2 = self.cell["a2"] * BOHR2A
+      a3 = self.cell["a3"] * BOHR2A
+      nat = self.getNumberOfAtoms()
+      times = ix * iy * iz
+      if times > 1:
+         nat *= times
+      #generate xyz data
+      xyz = str(nat) + '\n\n'
+      for atom in self.atoms:
+         if times:
+            for i in range(ix):
+               for j in range(iy):
+                  for k in range(iz):
+                     xyz += atom.symbol + " " + " ".join(
+                        map(str, atom.position * BOHR2A + i * a1 + j * a2 + k * a3)) + '\n'
+      #creat viewer
+      xyzview = py3Dmol.view(width=width, height=height)
+      xyzview.addModel(xyz, 'xyz')
+      if debug:
+         print(xyz)
+      xyzview.setStyle({style: {}})
+      #draw the box
+      a0 = np.array([0.0, 0.0, 0.0])
+      from_ = [a0, a1 + a2, a1 + a3, a2 + a3]
+      to_ = [[a1, a2, a3], [a1, a2, a1 + a2 + a3], [a1, a3, a1 + a2 + a3], [a2, a3, a1 + a2 + a3]]
+      for frm, li_to in zip(from_, to_):
+         x0, y0, z0 = frm
+         for to in li_to:
+            x1, y1, z1 = to
+            xyzview.addLine(
+               {'color': 'blue', 'start': {'x': x0, 'y': y0, 'z': z0}, 'end': {'x': x1, 'y': y1, 'z': z1}});
+      #show
+      xyzview.zoomTo()
+      xyzview.show()
+
+
+
+
+
+