pyemaps 2.0.0__py3-none-any.whl

pyemaps/diffract/mxtal_dec.py

@@ -0,0 +1,201 @@
+'''
+.. This file is part of pyEMAPS
+ 
+.. ----
+
+.. pyEMAPS is free software. You can redistribute it and/or modify 
+.. it under the terms of the GNU General Public License as published 
+.. by the Free Software Foundation, either version 3 of the License, 
+.. or (at your option) any later version..
+
+.. pyEMAPS is distributed in the hope that it will be useful,
+.. but WITHOUT ANY WARRANTY; without even the implied warranty of
+.. MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+.. GNU General Public License for more details.
+
+.. You should have received a copy of the GNU General Public License
+.. along with pyEMAPS.  If not, see `<https://www.gnu.org/licenses/>`_.
+
+.. Contact supprort@emlabsoftware.com for any questions and comments.
+
+.. ----
+
+
+Author:             EMLab Solutions, Inc.
+Date Created:       May 07, 2022  
+
+'''
+def add_mxtal(target):
+    from . import dif
+    from .. import (ID_MATRIX, MLEN, DEF_CELLBOX, 
+                   DEF_XZ, DEF_ORSHIFT, DEF_TRSHIFT,
+                   DEF_LOCASPACE)
+    from .. import MxtalError
+    from ..fileutils import compose_ofn
+    from ..xtal import Xtal
+    
+    @staticmethod
+    def printXYZ( mx):
+        '''
+        Print mxtal data in .xyz format in standard output. 
+        Refer to `XYZ format <https://wiki.jmol.org/index.php/File_formats/Formats/XYZ>`_
+        for its definition and usage.
+        
+        :param mx: Crystal structure object defined in xtal.py defiend as Xtal. 
+        :type mx: Xtal, required
+
+        .. note:: An example of Silicon atomic structure by pyemaps:
+            
+        .. code-block:: console
+
+            216
+                50.0 50.0 50.0 90.0 90.0 90.0
+            SI        	 0.6788375000   0.6788375000   0.6788375000 
+            SI        	 3.3941875000   3.3941875000   0.6788375000 
+            SI        	 4.7518625000   2.0365125000   2.0365125000 
+            SI        	 2.0365125000   4.7518625000   2.0365125000 
+            SI        	 3.3941875000   0.6788375000   3.3941875000 
+            ...
+
+        '''
+        if not isinstance(mx, Xtal): 
+            raise MxtalError("The print object is not valid atomic structure object.")
+        print(f'{str(mx)}')
+
+    def writeXYZ(self, mx, fn=None):
+        '''
+        Save crystal structure object data generated by pyemaps to a .xyz file <fn>
+        File path is composed by pyemaps depending on whether 
+        PYEMAP_DATA environment variable is set. For details how
+        *pyemaps* compose the file name see 
+        :ref:`Environment Variables <Environment Variables>`
+        for details.
+        
+        The file can be imported into external tool such as Jmole to
+        view its content. 
+        
+        :param mx: Crystal structure object defined in xtal.py defiend as Xtal. 
+        :type mx: Xtal, required
+
+        :param fn: file name for data to be saved. 
+        :type fn: str, optional
+
+        '''
+        
+        if not isinstance(mx, Xtal): 
+            raise MxtalError("The print object is not valid atomic structure object.")
+        
+
+        xyzfn = compose_ofn(fn, self.name, ty='mxtal') +'.xyz'
+        
+        try:
+            with open(xyzfn, 'w') as f:
+                f.writelines(str(mx))
+        except (FileNotFoundError, IOError, PermissionError) as e:
+            print(f'Error writing xyz data file {fn}')
+            return -1
+        except Exception:
+            return -1
+        else:
+            print(f'Successfully saved mxtal data in file: {xyzfn}')
+            return 0
+
+    def generateMxtal(self, 
+                      trMatrix = ID_MATRIX, 
+                      trShift = DEF_TRSHIFT, #Transformation shift
+                      cellbox = DEF_CELLBOX,
+                      xz = DEF_XZ,
+                      orShift = DEF_ORSHIFT, #Origin shift
+                      locASpace = DEF_LOCASPACE,
+                      bound = None): #location in A Space
+        """
+        Generate the crystal atomic structure data in .xyz format.
+
+        :param trMatrix: Transformation matrix
+        :type trMatrix: array, optional
+
+        :param trShift: Transformation shift
+        :type trShift: array, optional
+
+        :param cellbox: Locate atoms inside a box defined. 
+        :type cellbox: array, optional
+
+        :param xz: X and Z orientations in real space. 
+        :type xz: array, optional
+
+        :param orShift: Origin shift. 
+        :type orShift: float, optional
+
+        :param locASpace: Locate atoms inside a box defined. 
+        :type locASpace: array, optional
+
+        :param bound: Location in A Space. 
+        :type bound: float, optional
+        
+        :return: a crystal structure object
+        :rtype: :py:mod:`pyemaps.Xtal` class
+
+        """
+        import numpy as np
+        from numpy import asfortranarray as farray
+        from . import mxtal as MX
+
+        dif.initcontrols()
+        
+        self.load(cty=1)
+            
+        tmat = farray(np.array(trMatrix))
+        
+        pxz = farray(np.array(xz))
+
+        if bound is not None:
+            ret = MX.do_mxtal(tmat, trShift, cellbox[0], cellbox[1],
+                            pxz[0], pxz[1], orShift, locASpace, bound)
+        else:
+            ret = MX.do_mxtal(tmat, trShift, cellbox[0], cellbox[1],
+                            pxz[0], pxz[1], orShift, locASpace)
+        
+        if ret != 1:
+            raise MxtalError('Failed to starting mxtal module')
+        
+        na = MX.get_nxyz()
+        
+        if na <=0:
+            raise MxtalError('Failed to generate data')
+
+        xyz, ret = MX.get_xyzdata(na)
+    
+        if ret != 1:
+            raise MxtalError('Failed to retrieve data')
+
+        sym = farray(np.empty((MLEN, na), dtype='c'))
+        sym, ret = MX.get_symdata(sym)
+    
+        if ret != 1:
+            raise MxtalError('Failed to retrieve data')
+
+        tsym = np.transpose(sym)
+        txyz = np.transpose(xyz)
+        
+        mx = Xtal()
+        for i in range(na):          
+            s = bytearray(tsym[i]).decode('utf-8').strip(" \x00")
+            
+            mx.add(s, txyz[i])
+
+        nc = 6
+        cell, ret = MX.get_cellconst(nc)
+        
+        mx.cell = cell
+
+        if ret !=0:
+            raise MxtalError(f'Failed to retrieve cell constants: {ret}')
+
+        # clean up
+        MX.cleanup()
+        return mx
+
+    target.generateMxtal = generateMxtal
+    target.printXYZ = printXYZ
+    target.writeXYZ =writeXYZ
+    return target

pyemaps/diffract/powder_dec.py

@@ -0,0 +1,137 @@
+'''
+.. This file is part of pyEMAPS
+ 
+.. ----
+
+.. pyEMAPS is free software. You can redistribute it and/or modify 
+.. it under the terms of the GNU General Public License as published 
+.. by the Free Software Foundation, either version 3 of the License, 
+.. or (at your option) any later version..
+
+.. pyEMAPS is distributed in the hope that it will be useful,
+.. but WITHOUT ANY WARRANTY; without even the implied warranty of
+.. MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+.. GNU General Public License for more details.
+
+.. You should have received a copy of the GNU General Public License
+.. along with pyEMAPS.  If not, see `<https://www.gnu.org/licenses/>`_.
+
+.. Contact supprort@emlabsoftware.com for any questions and comments.
+
+.. ----
+
+.. Author:             EMLab Solutions, Inc.
+.. Date Created:       May 07, 2022  
+
+'''
+def add_powder(target):
+   
+    try:
+        from . import powder
+
+    except ImportError as e:               
+        print(f"Error: required module pyemaps.powder not found")
+        
+    def plotPowder(self, pw):
+
+        """
+        Show powder diffraction created from 
+        `generatePowder <pyemaps.crystals.html#pyemaps.crystals.Crystal.generatePowder>`_.
+
+        :param pw: Powder diffraction data
+        :type pw: array, required
+
+        """
+        import numpy as np
+        import matplotlib.pyplot as plt
+
+        xdim, _ = np.shape(pw)
+        if xdim !=2:
+            raise ValueError("Failed to plot: data error")
+        
+        fig, ax = plt.subplots()
+        # canvas.set_window_title was removed in matplotlib 3.6
+        if fig.canvas.manager is not None:
+            fig.canvas.manager.set_window_title('PYEMAPS')
+        fig.suptitle("Electron Powder Diffraction", fontsize=14, fontweight='bold')
+
+        ax.set_title(self.name)
+        
+        ax.set_ylabel('Intensity')
+        ax.set_xlabel('Scattering Angle 2\u03F4 (Rad)')
+        ax.plot(pw[0], pw[1], 'b')
+
+        plt.show()
+
+    def generatePowder(self,
+            kv = 100, 
+            t2max = 0.05, 
+            smax = 1.0, 
+            eta = 1.0, 
+            gamma = 0.001, 
+            absp = 0, 
+            bg = False,
+            bamp = 0.35, 
+            bgamma = 0.001, 
+            bmfact = 0.02):
+        '''
+        Generates powder diffraction.
+
+        :param kv: Accelaration voltage in kilo-volts.
+        :type kv: int or float, optional
+
+        :param t2max: Maximum scattering angle.
+        :type t2max: float, optional
+
+        :param smax: Maximum Sin(theta)/Wavelength.
+        :type smax: float, optional
+
+        :param smax: Maximum Sin(theta)/Wavelength.
+        :type smax: float, optional
+
+        :param eta: the mixing coefficient between gaussian and lorentzian in a pseudo-Voight peak function.
+        :type eta: float, optional
+
+        :param gamma: Diffraction peaks half maximum half width.
+        :type gamma: float, optional
+
+        :param absp: With Absoption structure factor (1 -default) or not (0).
+        :type absp: int, optional
+
+        :param isbgdon: Background on or not (default no background).
+        :type isbgdon: int, optional
+
+        :param bamp: Background amplitude.
+        :type bamp: float, optional
+
+        :param bgamma: Background width.
+        :type bgamma: float, optional
+
+        :param bmfact: Background exponential damping factor.
+        :type bmfact: float, optional
+
+        :return: an array of 2 x 1000 with the first row representing the scattering angle 2theta and the second the intensity
+        :rtype: array
+
+        '''     
+        import numpy as np
+        from numpy import asfortranarray as farray
+        
+        self.load()
+          
+        rawP = farray(np.zeros((2,1000), dtype=np.float32))
+       
+        ret = powder.generate_powder(rawP, kv=kv, t2max=t2max, 
+                smax = smax, eta=eta, gamma=gamma, isab = absp, 
+                isbgdon = bg, bamp = bamp, bgamma = bgamma, 
+                bmfact = bmfact)
+
+        if ret != 0:
+            print(f'Error generating powder data for {self.name}')
+
+        return rawP
+    
+    target.generatePowder = generatePowder
+    target.plotPowder = plotPowder
+
+    return target

pyemaps/diffract/stereo_dec.py

@@ -0,0 +1,111 @@
+'''
+.. This file is part of pyEMAPS
+ 
+.. ----
+
+.. pyEMAPS is free software. You can redistribute it and/or modify 
+.. it under the terms of the GNU General Public License as published 
+.. by the Free Software Foundation, either version 3 of the License, 
+.. or (at your option) any later version..
+
+.. pyEMAPS is distributed in the hope that it will be useful,
+.. but WITHOUT ANY WARRANTY; without even the implied warranty of
+.. MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+.. GNU General Public License for more details.
+
+.. You should have received a copy of the GNU General Public License
+.. along with pyEMAPS.  If not, see `<https://www.gnu.org/licenses/>`_.
+
+.. Contact supprort@emlabsoftware.com for any questions and comments.
+
+.. ----
+
+.. Author:             EMLab Solutions, Inc.
+.. Date Created:       May 07, 2022  
+
+'''
+def add_stereo(target):
+    def generateStereo(self, xa = (0,2,0), 
+                            tilt=(0.0,0.0),
+                            zone = (0, 0, 1)):
+        """
+        Generate stereodiagram.
+
+        :param xa: Crystal horizontal axis in reciprical space
+        :type xa: tuple of 3 integers, optional
+
+        :param tilt: Sample tilts in (x,y)
+        :type tilt: tuple, optional
+
+        :param zone: Zone axis
+        :type zone: tuple, optional
+
+        :return: A list of stereodiagram elements represented by dict object
+        :rtype: list of dict object
+
+        Example of the stereodiagram output:
+
+        .. code-block:: python
+
+            [
+                {
+                    "c": (x,y),              # center
+                    "r": 1.0,                # radius
+                    "idx": (h, k, l),        # Miller Index
+                }
+            ]    
+
+        To display the resulting stereodiagram, use 
+        `showStereo <pyemaps.display.html#pyemaps.display.showStereo>`_.
+        
+        """
+        from . import dif, stereo
+        
+        import numpy as np
+        from numpy import asfortranarray as farray
+
+        from ..errors import StereodiagramError 
+        from .. import DEF_XAXIS
+
+        dif.initcontrols()
+        dif.setzone(zone[0], zone[1], zone[2])        
+        
+        if xa != DEF_XAXIS:
+            dif.set_xaxis(1, xa[0], xa[1], xa[2])
+        dif.setsamplecontrols(tilt[0], tilt[1], 0.0, 0.0)
+
+        # load the crystal
+        
+        self.load()
+
+        ret = dif.diffract(3)
+        if ret != 1:
+            raise StereodiagramError('Stereodiagram generation failed')
+
+        sl = stereo.get_stereolimit()
+
+        sdata = farray(np.zeros((6, sl)), dtype=float)
+      
+        sdata, ns, ret = stereo.do_stereogram(sdata)
+
+        if ret != 1:
+            raise StereodiagramError('Stereodiagram generation failed')
+
+        stereo_list = []
+        for i in range(ns):
+            item = {}
+            s = sdata[0:, i]
+            item['c'] = (s[0], s[1])
+            item['r'] = s[2]
+            item['idx'] = (s[3], s[4],s[5])
+            stereo_list.append(item)
+
+        #release the memory
+        dif.diff_internaldelete(0)
+        dif.diff_delete()
+        
+        return stereo_list
+        
+    target.generateStereo = generateStereo
+    
+    return target