stm-sim 0.1__tar.gz

stm_sim-0.1/LICENSE

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+MIT License
+
+Copyright (c) 2024 pj.ren
+
+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.

stm_sim-0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: stm_sim
+Version: 0.1
+Summary: An STM simulation python library.
+Home-page: https://gitee.com/pjren/stm_sim
+Author: Renpj
+Author-email: 0403114076@163.com
+License: MIT
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: ase
+
+# stm_sim
+ 
+An STM simulation python library from PARCHG by VASP.
+Please check the example code in example folder.
+

stm_sim-0.1/README.md

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+# stm_sim
+ 
+An STM simulation python library from PARCHG by VASP.
+Please check the example code in example folder.
+

stm_sim-0.1/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

stm_sim-0.1/setup.py

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+from setuptools import setup
+
+with open("README.md", "r", encoding='utf-8') as f:
+    long_description = f.read()
+
+install_requires = [
+    'ase',
+]
+
+setup(
+    name='stm_sim',
+    version='0.1',
+    packages=['stm_sim'],
+    url='https://gitee.com/pjren/stm_sim',
+    license='MIT',
+    author='Renpj',
+    author_email='0403114076@163.com',
+    description='An STM simulation python library.',
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    install_requires=install_requires,
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "Operating System :: OS Independent",
+    ],
+)

stm_sim-0.1/stm_sim/stm.py

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+import numpy as np
+from ase.calculators.vasp import VaspChargeDensity
+from ase.dft.stm import dos2current
+
+
+class STM:
+    """
+    Get STM from VASP PARCHG.
+
+    TODO: Export 2d data for external program plot.
+    """
+
+    def __init__(self, bias=None):
+        self.atoms = None
+        self.density = None
+        self.ngridpoints = np.array([0, 0, 0])
+        if bias is None or bias == 0:
+            "TODO: Read from INCAR EINT"
+            self.bias = 0.1
+            self.bias_range = (0, 0.1)
+        elif type(bias) in (list, tuple):
+            self.bias = np.abs(bias).max()
+            self.bias_range = bias
+        elif type(bias) in (float, int):
+            self.bias = bias
+            self.bias_range = sorted((0, bias))
+        self.height = None
+        self.scan_mode = None
+        self.x, self.y, self.data = None, None, None
+
+    def read_parchg(self, filename='PARCHG'):
+        print("Reading PARCHG file now...\n")
+        vasp_charge = VaspChargeDensity(filename)
+        self.density = vasp_charge.chg[-1]
+        self.atoms = vasp_charge.atoms[-1]
+        self.ngridpoints = np.array(self.density.shape)
+        # Read scaling factor and unit cell of the crystal structure.
+        self.unit_cell = self.atoms.get_cell()
+        self.cell_lengths = np.sqrt(np.dot(self.unit_cell, self.unit_cell.transpose()).diagonal())
+        self.zinterval = self.cell_lengths[2] / self.ngridpoints[2]
+
+        del vasp_charge
+        print("Done!\n")
+
+    def scan_current(self, height=None, bottom=False, repeat=(1, 1), plot=True, startpoint=None):
+
+        if height is None:
+            height = 2
+        if bottom:
+            height = self.atoms.positions[:, 2].min() - height
+        else:
+            height = self.atoms.positions[:, 2].max() + height
+
+        self.scan_mode = 'constant_current'
+        self.height = height
+
+        n2 = height / self.cell_lengths[2] * self.ngridpoints[2]  # this means scanning must be in c direction
+        dn2 = n2 - np.floor(n2)
+        n2 = int(n2) % self.ngridpoints[2]
+        # Get the averaged current. 这里使用的是 最大/最小值的平均值，而不是总的平均值
+        averaged_current = ((1 - dn2) * self.density[:, :, n2].ptp()
+                            + dn2 * self.density[:, :, (n2 + 1) % self.ngridpoints[2]].ptp())
+        averaged_current = dos2current(self.bias, averaged_current)
+        density = self.density.reshape((-1, self.ngridpoints[2]))
+        density = dos2current(self.bias, density)
+        heights = self.find_heights(density, averaged_current, bottom=bottom, startpoint=startpoint)
+        s0 = heights.shape = self.density.shape[:2]
+        heights = np.tile(heights, repeat)
+        s = heights.shape
+
+        ij = np.indices(s, dtype=float).reshape((2, -1)).T
+        x, y = np.dot(ij / s0, self.atoms.cell[:2, :2]).T.reshape((2,) + s)
+
+        self.x = x
+        self.y = y
+        self.data = heights
+
+        if plot:
+            self.plot(x, y, heights, reverse=bottom, absolute=True)
+        return x, y, heights
+
+    def find_heights(self, density, current, bottom=False, startpoint=None):
+        assert current > 0
+        heights = np.empty(density.shape[0])
+        self.current = current
+        for i, den in enumerate(density):
+            if bottom:
+                n = 1
+                if startpoint is not None:
+                    n = int(startpoint * self.ngridpoints[2])
+                while n < self.ngridpoints[2]:
+                    if den[n] > current:
+                        break
+                    n += 1
+                else:
+                    n = 1
+                c1, c2 = den[n-1:n+1]
+                heights[i] = (n - (c2 - current) / (c2 - c1)) * self.zinterval
+            else:
+                n = self.ngridpoints[2] - 1
+                if startpoint is not None:
+                    n = int(startpoint * self.ngridpoints[2])
+                while n > 0:
+                    if den[n] > current:
+                        break
+                    n -= 1
+                else:
+                    n = self.ngridpoints[2] - 1
+                c2, c1 = den[n:n+2]
+                heights[i] = (n + (c2 - current) / (c2 - c1)) * self.zinterval
+            if not c1 <= current <= c2:
+                if i != 0:
+                    heights[i] = heights[i-1]
+                else:
+                    raise ValueError("Density values error!")
+        return heights
+
+    def scan_height(self, height=None, repeat=(1, 1), bottom=False, plot=True, startpoint=None):
+        if height is None:
+            height = 2
+        if bottom:
+            height = self.atoms.positions[:, 2].min() - height
+        else:
+            height = self.atoms.positions[:, 2].max() + height
+
+        self.scan_mode = 'constant_height'
+        self.height = height
+
+        nz = self.ngridpoints[2]
+        ldos = self.density.reshape((-1, nz))
+
+        I = np.empty(ldos.shape[0])
+
+        zp = height / self.atoms.cell[2, 2] * nz
+        dz = zp - np.floor(zp)
+        zp = int(zp) % nz
+
+        for i, a in enumerate(ldos):
+            I[i] = dos2current(self.bias, (1 - dz) * a[zp] + dz * a[(zp + 1) % nz])
+
+        s0 = I.shape = self.density.shape[:2]
+        I = np.tile(I, repeat)
+        s = I.shape
+
+        ij = np.indices(s, dtype=float).reshape((2, -1)).T
+        x, y = np.dot(ij / s0, self.atoms.cell[:2, :2]).T.reshape((2,) + s)
+
+        self.x = x
+        self.y = y
+        self.data = I
+
+        if plot:
+            self.plot(x, y, I)
+        # Return scan with axes in Angstrom.
+        return x, y, I
+
+    def dI_dz(self, scan_mode='constant_current', height=None, bottom=False, repeat=(1, 1), startpoint=None):
+        assert scan_mode == self.scan_mode
+
+        if scan_mode == 'constant_height':
+            if self.x is None or height != self.height:
+                self.x, self.y, self.data = self.scan(scan_mode=scan_mode, height=height,
+                                                      bottom=bottom, repeat=repeat, startpoint=startpoint, plot=False)
+            height_plus = self.height + self.zinterval
+            data_plus = self.scan(scan_mode='constant_height', height=height_plus,
+                                  bottom=bottom, repeat=repeat, startpoint=startpoint)[-1]
+            dI = data_plus - self.data
+
+        elif scan_mode == 'constant_current':
+            if (repeat[0] != 1 or repeat[1] != 1) or self.x is None or height != self.height:
+                self.x, self.y, self.data = self.scan(scan_mode='constant_current', height=height,
+                                                      bottom=bottom, repeat=(1, 1), startpoint=startpoint, plot=False)
+            height_plus = self.data + self.zinterval
+            nz = self.ngridpoints[2]
+            ldos = self.density.reshape((-1, nz))
+            height_plus = height_plus.reshape((-1,))
+
+            I = np.empty(ldos.shape[0])
+            zp = height_plus / self.atoms.cell[2, 2] * nz
+            dz = zp - np.floor(zp)
+            zp = np.asarray(zp, int) % nz
+
+            for i, a in enumerate(ldos):
+                I[i] = dos2current(self.bias, (1 - dz[i]) * a[zp[i]] + dz[i] * a[(zp[i] + 1) % nz])
+
+            s0 = I.shape = self.density.shape[:2]
+            data_plus = np.tile(I, repeat)
+            dI = data_plus - self.current
+
+        return dI / self.zinterval
+
+    def scan(self, scan_mode='constant_current', height=None, bottom=False, repeat=(1, 1), plot=True, startpoint=None):
+        scan_mode_options = ['constant_height', 'constant_current']
+        if scan_mode not in scan_mode_options:
+            raise ValueError("Scan mode options: ", scan_mode_options)
+
+        if scan_mode == 'constant_current':
+            scan_func = self.scan_current
+        elif scan_mode == 'constant_height':
+            scan_func = self.scan_height
+        data = scan_func(height=height, bottom=bottom, repeat=repeat, plot=plot, startpoint=startpoint)
+        return data
+
+    def plot(self, x, y, data, scan_mode=None, reverse=False, absolute=False):
+        """
+        Suggest colormap: afmhot, gist_heat
+        :param absolute:
+        :param y:
+        :param x:
+        :param reverse:
+        :param scan_mode: constant_height, constant_current
+        :param data:
+        :return:
+        """
+        import matplotlib
+        matplotlib.use('Agg')
+        import matplotlib.pyplot as plt
+        # import matplotlib.cm as cm
+
+        if scan_mode is None:
+            scan_mode = self.scan_mode
+
+        plt.figure()
+        plt.rcParams['figure.max_open_warning'] = 50
+        plt.gca(aspect='equal')
+        plt.axis('off')
+        plt.xticks(())
+        plt.yticks(())
+        cm = plt.cm.get_cmap('%s' % 'gist_heat')
+        if not absolute:
+            if scan_mode == 'constant_current':
+                if reverse:
+                    minh = data.max()  # reference point
+                    data = minh - data
+                else:
+                    minh = data.min()
+                    data = data - minh
+        plt.contourf(x, y, data, 900, cmap=cm)
+        plt.colorbar()
+        if scan_mode == 'constant_height':
+            mode_label = 'H'
+        elif scan_mode == 'constant_current':
+            mode_label = 'C'
+        else:
+            mode_label = 'None'
+            print("Not support scan mode,", scan_mode)
+        plt.savefig(mode_label + '_' + str(round(self.height, 3)) + '.png', dpi=300, bbox_inches='tight')

stm_sim-0.1/stm_sim.egg-info/PKG-INFO

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+Metadata-Version: 2.1
+Name: stm_sim
+Version: 0.1
+Summary: An STM simulation python library.
+Home-page: https://gitee.com/pjren/stm_sim
+Author: Renpj
+Author-email: 0403114076@163.com
+License: MIT
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: ase
+
+# stm_sim
+ 
+An STM simulation python library from PARCHG by VASP.
+Please check the example code in example folder.
+

stm_sim-0.1/stm_sim.egg-info/SOURCES.txt

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+LICENSE
+README.md
+setup.py
+stm_sim/__init__.py
+stm_sim/stm.py
+stm_sim.egg-info/PKG-INFO
+stm_sim.egg-info/SOURCES.txt
+stm_sim.egg-info/dependency_links.txt
+stm_sim.egg-info/requires.txt
+stm_sim.egg-info/top_level.txt

stm_sim-0.1/stm_sim.egg-info/dependency_links.txt

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+

stm_sim-0.1/stm_sim.egg-info/requires.txt

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+ase

stm_sim-0.1/stm_sim.egg-info/top_level.txt

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+stm_sim