Chemical-Pressure-Plotter 0.6__tar.gz

chemical_pressure_plotter-0.6/Chemical Pressure Plotting/Plotting Chemical Pressures.py

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+import pyvista as pv
+import numpy as np
+
+plotter = pv.Plotter()
+#File Names must be input here
+Filenameroot=''
+Filenamexyz=f'{Filenameroot}_static_o_DS2_DEN.xyz'
+Filenamecoeff=f'{Filenameroot}_static-coeff'
+Filenamecell=f'{Filenameroot}_static-cell'
+Filenamegeo=f'{Filenameroot}_static-geo'
+
+#=======================================================================
+#=================Preferred Methods Of Scaling==========================
+#=======================================================================
+#Both of ScaleLobe and Scaleatom are controlled by sliders in the rendered chemical pressure
+ScaleLobe=100 #Scales the size of the chemical pressure lobes. Default is 100
+Scaleatom=1  #Can adjust for the size of atoms. Default is 1, 
+
+unitcelllinewidth=5 #Default is 5
+
+#Notes
+# This code works for 4 element compounds
+# This code does not work for compounds with more than 4 elements 
+# For help with this code contact the Fredrickson Group at UW Madison
+
+#Reading xyz from the xyz file.
+def ReadTxt(Filenamexyz):
+    with open(f"{Filenamexyz}", 'r') as f:
+        lines = f.readlines()
+        nameofatoms = []
+        for i, line in enumerate(lines):
+            line = line.strip().split()
+            line= [var.split("'") for var in line]
+            line=[element for var in line for element in var if element != '']
+            if i == 0:
+                num_atoms =int(line[0])
+                xyz= np.zeros((num_atoms,3))
+            elif i ==1:
+                continue
+            else:
+                coords = line[1:]
+                xyz[i-2, :] = np.array([float(coord) for coord in coords])
+            nameofatoms.append(line[0])
+        del(nameofatoms[0])
+        return xyz,nameofatoms
+xyz,nameofatoms=ReadTxt(Filenamexyz)
+atom1=nameofatoms[0] 
+atom2=0
+
+#This finds and labels each atom in the system 
+atoms={}
+count=0
+for thing in nameofatoms:
+    if thing not in atoms.keys():
+        atoms[thing] = count
+        count+=1
+
+#This converts the strings in the nameofatoms list to numbers in order to be read below.
+#Converts atom1 to 0, atom2 to 1, atom3 to 2, and atom4 to 3
+numberofatoms=[]
+numberofatoms = [atoms[s] for s in nameofatoms]
+
+#Getting coeff out of the coeff file
+def ReadTxt2(Filenamecoeff):
+    with open(f"{Filenamecoeff}", 'r') as f:
+        lines = f.readlines()
+        coeffvalues = []
+        for i, line in enumerate(lines):
+            line = line.strip().split()
+            line= [var.split("'") for var in line]
+            line=[element for var in line for element in var if element != '']
+            del(line[0])
+            line = [float(s) for s in line]
+            coeffvalues.append(line[0])
+        return coeffvalues
+coeffvalues=ReadTxt2(Filenamecoeff)
+
+#Changing Coeff to be a list of lists for the next step
+CPcoeff_temporary = []
+for i in range(len(coeffvalues) // 49):
+    CPcoeff_temporary.append([])
+    for j in range(49):
+        CPcoeff_temporary[i].append(coeffvalues[49 * i + j])
+
+coeffvalues = CPcoeff_temporary
+
+#Getting cell out of the cell file
+def ReadTxt3(Filenamecell):
+    cellvalues = []
+    with open(Filenamecell, 'r') as f:
+        for line in f:
+            parts = line.strip().split()
+            if len(parts) != 3:
+                raise ValueError("Each line must contain exactly 3 numbers")
+            cellvalues.append([float(x) for x in parts])
+    return np.array(cellvalues)
+cellvalues= ReadTxt3(Filenamecell)
+
+#getting the geo out of the file
+def ReadTxt4(filename):
+    geoelements = []
+    geovalues = []
+    with open(filename, 'r') as f:
+        for i, line in enumerate(f, start=1):
+            parts = line.strip().split()
+
+            if len(parts) != 4:
+                raise ValueError(f"Line {i} does not contain exactly 4 values")
+            
+            numbers = [float(parts[1]), float(parts[2]), float(parts[3])]
+
+            geoelements.append(parts[0])
+            geovalues.append(numbers)
+
+        return geoelements, np.array(geovalues, dtype=float)
+geoelements, geovalues=ReadTxt4(Filenamegeo)
+
+#This generates the chemical pressure values
+def Chemicalpressure(coeffvalues):
+    Geo_Cps =[]
+    for val in coeffvalues:
+        scale=1    #Use the scales at the top of the code this scales unpredictably
+
+        positive_surf = pv.ParametricEllipsoid(xradius = 1, yradius = 1, zradius = 1,)
+        negative_surf = pv.ParametricEllipsoid(xradius = 1, yradius = 1, zradius = 1,)
+        for i in range(len(positive_surf.points)):
+            r=0
+            x = positive_surf.points[i][0]
+            y = positive_surf.points[i][1]
+            z = positive_surf.points[i][2]
+            theta = np.arccos(z)
+
+            phi=0
+            if((theta > 0) and (theta < 3.14159)): 
+                if(x/np.sin(theta) > 1): 
+                    phi = 0
+                elif(x/np.sin(theta) < -1):
+                    phi = np.pi
+                else:
+                    phi = np.arccos(x/np.sin(theta))
+
+            if y < 0:
+                phi = -phi
+            #This is a Legendre Polynomial expansion. It goes to L=4 this can be expanded
+            #for additional quality. 
+
+            #L = 0
+            r += scale * 0.5 * (1 / np.pi)**0.5 * val[0]
+
+            #L = 1
+            r += scale * 0.5 * (3 / np.pi)**0.5 * np.cos(theta) * val[1]
+            r += -scale * (3 / (8 * np.pi))**0.5 * np.sin(theta) * np.cos(phi) * np.sqrt(2) * val[2]
+            r += -scale * (3 / (8 * np.pi))**0.5 * np.sin(theta) * np.sin(phi) * np.sqrt(2) * val[3]
+
+            #L = 2
+            r += scale * 0.25 * (5 / np.pi)**0.5 * (3*np.cos(theta)**2 - 1) * val[4]
+            r += -scale * 0.5 * (15 / np.pi)**0.5 * np.sin(theta) * np.cos(phi) * np.cos(theta) * val[5]
+            r += -scale * 0.5 * (15 / np.pi)**0.5 * np.sin(theta) * np.sin(phi) * np.cos(theta) * val[6]
+            r += scale * 0.25 * (15 / np.pi)**0.5 * np.sin(theta)**2 * np.cos(2*phi) * val[7]
+            r += scale * 0.25 * (15 / np.pi)**0.5 * np.sin(theta)**2 * np.sin(2*phi) * val[8]
+
+            #L = 3
+            r += scale * 0.25 * (7 / np.pi)**0.5 * (5*np.cos(theta)**3 - 3*np.cos(theta)) * val[9]
+            r += -scale * 0.125 * (21 / np.pi)**0.5 * np.sin(theta) * (5*np.cos(theta)**2 - 1) * np.cos(phi) * np.sqrt(2) * val[10]
+            r += -scale * 0.125 * (21 / np.pi)**0.5 * np.sin(theta) * (5*np.cos(theta)**2 - 1) * np.sin(phi) * np.sqrt(2) * val[11]
+            r += scale * 0.25 * (105 / (2*np.pi))**0.5 * np.sin(theta)**2 * np.cos(theta) * np.cos(2*phi) * np.sqrt(2) * val[12]
+            r += scale * 0.25 * (105 / (2*np.pi))**0.5 * np.sin(theta)**2 * np.cos(theta) * np.sin(2*phi) * np.sqrt(2) * val[13]
+            r += -scale * 0.125 * (35 / np.pi)**0.5 * np.sin(theta)**3 * np.cos(3*phi) * np.sqrt(2) * val[14]
+            r += -scale * 0.125 * (35 / np.pi)**0.5 * np.sin(theta)**3 * np.sin(3*phi) * np.sqrt(2) * val[15]
+
+            #L = 4
+            r += scale * (3/16) * (1 / np.pi)**0.5 * (35*np.cos(theta)**4 - 30*np.cos(theta)**2 + 3) * val[16]
+            r += -scale * (3/8) * (5 / np.pi)**0.5 * np.sin(theta) * (7*np.cos(theta)**3 - 3*np.cos(theta)) * np.cos(phi) * np.sqrt(2) * val[17]
+            r += -scale * (3/8) * (5 / np.pi)**0.5 * np.sin(theta) * (7*np.cos(theta)**3 - 3*np.cos(theta)) * np.sin(phi) * np.sqrt(2) * val[18]
+            r += scale * (3/8) * (5 / (2*np.pi))**0.5 * np.sin(theta)**2 * (7*np.cos(theta)**2 - 1) * np.cos(2*phi) * np.sqrt(2) * val[19]
+            r += scale * (3/8) * (5 / (2*np.pi))**0.5 * np.sin(theta)**2 * (7*np.cos(theta)**2 - 1) * np.sin(2*phi) * np.sqrt(2) * val[20]
+            r += -scale * (3/8) * (35 / np.pi)**0.5 * np.sin(theta)**3 * np.cos(theta) * np.cos(3*phi) * np.sqrt(2) * val[21]
+            r += -scale * (3/8) * (35 / np.pi)**0.5 * np.sin(theta)**3 * np.cos(theta) * np.sin(3*phi) * np.sqrt(2) * val[22]
+            r += scale * (3/16) * (35 / (2*np.pi))**0.5 * np.sin(theta)**4 * np.cos(4*phi) * np.sqrt(2) * val[23]
+            r += scale * (3/16) * (35 / (2*np.pi))**0.5 * np.sin(theta)**4 * np.sin(4*phi) * np.sqrt(2) * val[24]
+
+            r *= 4 * np.pi
+
+            if r < 0:
+                positive_surf.points[i] = np.zeros(3).copy()
+                negative_surf.points[i]= np.array([ r * np.sin(theta) * np.cos(phi), 
+                                                    r * np.sin(theta) * np.sin(phi),
+                                                    r * np.cos(theta)]).copy()
+            else:
+                negative_surf.points[i] = np.zeros(3).copy()
+                positive_surf.points[i]= np.array([ r * np.sin(theta) * np.cos(phi), 
+                                                    r * np.sin(theta) * np.sin(phi),
+                                                    r * np.cos(theta)]).copy()
+        Geo_Cps.append([positive_surf,negative_surf])
+
+    return Geo_Cps
+
+Geo_Cps = Chemicalpressure(coeffvalues)
+atom_data = []
+#Graphing the spheres just the atom location
+for i, coords in enumerate(xyz):
+    Sphere = pv.Sphere()
+    orig_pts = Sphere.points.copy()
+    Sphere.points *=Scaleatom
+    Sphere=Sphere.translate(coords, inplace=True)
+    if numberofatoms[i] == 0:
+        plotter.add_mesh(Sphere, color='blue')
+    elif numberofatoms[i] == 1:
+        plotter.add_mesh(Sphere, color='red')
+    elif numberofatoms[i] == 2:
+        plotter.add_mesh(Sphere, color='orange')
+    else:  #If more than 4 atoms are needed increase the size of this section to the number of atoms needed
+        plotter.add_mesh(Sphere, color='green')
+    atom_data.append((Sphere, orig_pts, np.array(coords)))
+    
+#Needed for scaling
+lobe_data = []
+
+#Appling the chemical presure lobe
+def apply_CP(geovalues, cellvalues, Geo_Cps, xyz):
+    natoms_geo = len(geovalues)
+    natoms_coords = len(xyz)
+    for j1 in range(-4, 5):
+        for j2 in range(-4, 5):
+            for j3 in range(-4, 5):
+                for k1 in range(natoms_geo):
+                    for k2 in range(natoms_coords):
+                        x1 = (geovalues[k1][0] + cellvalues[0][0]*j1 +cellvalues[1][0]*j2 +cellvalues[2][0]*j3)
+                        y1 = (geovalues[k1][1] + cellvalues[0][1]*j1 + cellvalues[1][1]*j2 + cellvalues[2][1]*j3)
+                        z1 = (geovalues[k1][2] + cellvalues[0][2]*j1 + cellvalues[1][2]*j2 + cellvalues[2][2]*j3)
+                        x2 = xyz[k2][0]
+                        y2 = xyz[k2][1]
+                        z2 = xyz[k2][2]
+                        dist = ((x1-x2)**2 + (y1-y2)**2 + (z1-z2)**2)**0.5 #This filters out all objects that are on top of other objects should filter to the number of atoms past this point
+                        if(dist < 0.1): 
+                            for i in range(0,1):
+                                ScaleXYZ=1  #This can be ignored do not change from 1, 
+                                #this changes how much the chemical pressures scale if changed from 1 
+                                #only use for bug fixes
+                                xyztemp=[x2/ScaleXYZ,y2/ScaleXYZ,z2/ScaleXYZ]
+                                ellipsoid1 = Geo_Cps[k1][1].copy() # negative lobe
+                                ellipsoid2 = Geo_Cps[k1][0].copy() # positive lobe
+
+                                orig_pts1 = ellipsoid1.points.copy()
+                                orig_pts2 = ellipsoid2.points.copy()
+
+                                ellipsoid1.points *= ScaleLobe  
+                                ellipsoid2.points *= ScaleLobe
+                            
+                                ellipsoid1.translate(xyztemp, inplace=True)
+                                ellipsoid2.translate(xyztemp, inplace=True)
+
+                                lobe_data.append((ellipsoid1, orig_pts1,xyztemp))
+                                lobe_data.append((ellipsoid2, orig_pts2,xyztemp))
+                            
+                                plotter.add_mesh(ellipsoid1, style='surface', color='black')  #Black in website code,  Negative
+                                plotter.add_mesh(ellipsoid2, style='surface', color='white')  #White in website code,  Positive
+
+CreateCPs = apply_CP(geovalues, cellvalues, Geo_Cps, xyz)
+#Sliders that scaleatoms and scale the chemical pressure lobes
+def Scale_lobes(value):
+    for mesh, orig_pts, center in lobe_data:
+        mesh.points = orig_pts *value +center
+    plotter.render()
+
+plotter.add_slider_widget(
+    callback=Scale_lobes,
+    rng = [1,300],
+    value = ScaleLobe,
+    title= 'Scaling Lobes',
+    pointa=(0,0.1),
+    pointb=(0.4,0.1),
+)
+
+def scale_atoms(value):
+    for mesh, orig_pts, center in atom_data:
+        mesh.points = orig_pts *value +center
+    plotter.render()
+
+plotter.add_slider_widget(
+    callback=scale_atoms,
+    rng = [0.01,3],
+    value = Scaleatom,
+    title= 'Scaling Atoms',
+    pointa=(0,0.25),
+    pointb=(0.4,0.25),
+)
+
+#Creates points for the unit cell
+cellvalue0=cellvalues[0]
+cellvalue1=cellvalues[1]
+cellvalue2=cellvalues[2]
+
+Zero= np.array([0,0,0])
+cellvalue01 = cellvalue0 + cellvalue1
+cellvalue02 = cellvalue0 + cellvalue2
+cellvalue12 = cellvalue1 + cellvalue2
+cellvalue012 = cellvalue0 + cellvalue1 + cellvalue2
+
+unitcellpoints = np.array([Zero,cellvalue0,Zero,cellvalue1,cellvalue0,cellvalue01,cellvalue1,cellvalue01, #Bottom Face
+                           Zero,cellvalue2,cellvalue0,cellvalue02,cellvalue1,cellvalue12,cellvalue01,cellvalue012, #Vertical Edges
+                           cellvalue2,cellvalue02,cellvalue2,cellvalue12,cellvalue02,cellvalue012,cellvalue12,cellvalue012], #Top Face
+                           dtype=float)
+
+#Create lines for unit cell
+plotter.add_lines(unitcellpoints, color = 'green', width = unitcelllinewidth,)   #The value for the width can be changed at the top of the code
+plotter.show()

chemical_pressure_plotter-0.6/Chemical_Pressure_Plotter.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: Chemical-Pressure-Plotter
+Version: 0.6
+Summary: Uses python to plot chemical pressures of atomic compounds
+Home-page: https://github.com/ajsmits2/Chemical-Pressure/
+Download-URL: https://github.com/ajsmits2/Chemical-Pressure/archive/refs/tags/Chemistry.tar.gz
+Author: Alexander Smits
+Author-email: ajsmits2@wisc.edu
+License: MIT
+Keywords: Chemistry,Pressure,Chemical
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: Topic :: Software Development :: Build Tools
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.4
+Classifier: Programming Language :: Python :: 3.5
+Classifier: Programming Language :: Python :: 3.6
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: pyvista
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: download-url
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: summary

chemical_pressure_plotter-0.6/Chemical_Pressure_Plotter.egg-info/SOURCES.txt

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+LICENSE
+README.md
+setup.cfg
+setup.py
+Chemical Pressure Plotting/Plotting Chemical Pressures.py
+Chemical_Pressure_Plotter.egg-info/PKG-INFO
+Chemical_Pressure_Plotter.egg-info/SOURCES.txt
+Chemical_Pressure_Plotter.egg-info/dependency_links.txt
+Chemical_Pressure_Plotter.egg-info/requires.txt
+Chemical_Pressure_Plotter.egg-info/top_level.txt

chemical_pressure_plotter-0.6/Chemical_Pressure_Plotter.egg-info/dependency_links.txt

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+

chemical_pressure_plotter-0.6/Chemical_Pressure_Plotter.egg-info/requires.txt

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+numpy
+pyvista

chemical_pressure_plotter-0.6/Chemical_Pressure_Plotter.egg-info/top_level.txt

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+Chemical Pressure Plotting

chemical_pressure_plotter-0.6/LICENSE

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+MIT License
+
+Copyright (c) 2026 ajsmits2
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

chemical_pressure_plotter-0.6/PKG-INFO

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+Metadata-Version: 2.4
+Name: Chemical-Pressure-Plotter
+Version: 0.6
+Summary: Uses python to plot chemical pressures of atomic compounds
+Home-page: https://github.com/ajsmits2/Chemical-Pressure/
+Download-URL: https://github.com/ajsmits2/Chemical-Pressure/archive/refs/tags/Chemistry.tar.gz
+Author: Alexander Smits
+Author-email: ajsmits2@wisc.edu
+License: MIT
+Keywords: Chemistry,Pressure,Chemical
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: Topic :: Software Development :: Build Tools
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.4
+Classifier: Programming Language :: Python :: 3.5
+Classifier: Programming Language :: Python :: 3.6
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: pyvista
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: download-url
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: summary

chemical_pressure_plotter-0.6/README.md

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+This code plots chemical pressures in crystals.
+It will work with a maximum of 4 distinct atoms by default, although this can be changed. 
+Black lobes represent negative chemical pressures while white lobes represent positive chemical pressures. 
+The code requires a optimized crystal strucutre and the following files; a .xyz file, a coeff file, a cell file and a geo file.
+
+For help with this code contact the Fredrickson Group at the University of Wisconsin Madison

chemical_pressure_plotter-0.6/setup.cfg

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+[metadata]
+description-file = README.md
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

chemical_pressure_plotter-0.6/setup.py

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+from distutils.core import setup
+setup(
+  name = 'Chemical-Pressure-Plotter',         # How you named your package folder (MyLib)
+  packages = ['Chemical Pressure Plotting'],   # Chose the same as "name"
+  version = '0.6',      # Start with a small number and increase it with every change you make
+  license='MIT',        # Chose a license from here: https://help.github.com/articles/licensing-a-repository
+  description = 'Uses python to plot chemical pressures of atomic compounds',   # Give a short description about your library
+  author = 'Alexander Smits',                   # Type in your name
+  author_email = 'ajsmits2@wisc.edu',      # Type in your E-Mail
+  url = 'https://github.com/ajsmits2/Chemical-Pressure/',   # Provide either the link to your github or to your website
+  download_url = 'https://github.com/ajsmits2/Chemical-Pressure/archive/refs/tags/Chemistry.tar.gz',    # I explain this later on
+  keywords = ['Chemistry', 'Pressure', 'Chemical'],   # Keywords that define your package best
+  install_requires=[            # I get to this in a second
+          'numpy',
+          'pyvista',
+      ],
+  classifiers=[
+    'Development Status :: 5 - Production/Stable',      # Chose either "3 - Alpha", "4 - Beta" or "5 - Production/Stable" as the current state of your package
+
+    'Intended Audience :: Developers',      # Define that your audience are developers
+    'Topic :: Software Development :: Build Tools',
+
+    'License :: OSI Approved :: MIT License',   # Again, pick a license
+
+    'Programming Language :: Python :: 3',      #Specify which pyhton versions that you want to support
+    'Programming Language :: Python :: 3.4',
+    'Programming Language :: Python :: 3.5',
+    'Programming Language :: Python :: 3.6',
+  ],
+)