mdkits 0.1a4__tar.gz → 0.1.1__tar.gz

{mdkits-0.1a4 → mdkits-0.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 0.1a4
+Version: 0.1.1
 Summary: tools for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory
@@ -28,7 +28,25 @@ Description-Content-Type: text/markdown
 ```bash
 pip install mdkits --upgrade
 ```
+
 ### 密度分布
+`density`用于分析体系中的某种元素沿z轴的密度分布, 如分析体系中的`O`元素沿z轴的密度分布, `--element`选项指定元素使用`MDAnalysis`的[选择语言](https://userguide.mdanalysis.org/stable/selections.html):
+```bash
+mdkits density [FILENAME] --element="name H" --cell [FILENAME]
+```
+这样会输出一个文件名为`density_name_H.dat`的文件, 第一列为z轴坐标, 第二列为浓度分布, 单位为 mol/L. 如果想输出为单位为 $g/cm^3$ 的密度分布, 可以指定`--atomic_mass` 选项, 如:
+```bash
+mdkits density [FILENAME] --element="name H" --cell [FILENAME] --atomic_mass=1.00784
+```
+则输出单位为 $g/cm^3$ 的密度分布. 可以指定表面原子来将密度分布归一化到表面, 如:
+```bash
+mdkits density [FILENAME] --element="name O" --cell 10,10,10 --atomic_mass=18.01528 --surface="name Pt and name Ru"
+```
+这样会将密度分布归一化到表面, 同时以O原子的位置作为水分子的位置分析处理水分子的密度分布. 对于体系中存在 $OH^-$ 离子的体系可以使用`--update_water`的选项在每一帧更新水分子的位置, 不需要额外指定元素, 如:
+```bash
+mdkits density [FILENAME] --update_water --cell 10,10,10 --atomic_mass=18.01528 --surface="name Pt and name Ru"
+```
+输出的文件名为`density_water.dat`.
 
 ### 氢键
 
@@ -102,7 +120,7 @@ mdkits convert -c structure.cif -o structure_xyz
 1. `--nor`: 对数据进行归一化处理
 2. `--gaus`: 对数据进行高斯过滤
 3. `--fold`: 堆数据进行折叠平均
-4. `--err`: 计算数据的误差棒
+4. `--err`: 计算数据的误差棒   
 等
 
 ### 绘图工具

{mdkits-0.1a4 → mdkits-0.1.1}/README.md

@@ -3,7 +3,25 @@
 ```bash
 pip install mdkits --upgrade
 ```
+
 ### 密度分布
+`density`用于分析体系中的某种元素沿z轴的密度分布, 如分析体系中的`O`元素沿z轴的密度分布, `--element`选项指定元素使用`MDAnalysis`的[选择语言](https://userguide.mdanalysis.org/stable/selections.html):
+```bash
+mdkits density [FILENAME] --element="name H" --cell [FILENAME]
+```
+这样会输出一个文件名为`density_name_H.dat`的文件, 第一列为z轴坐标, 第二列为浓度分布, 单位为 mol/L. 如果想输出为单位为 $g/cm^3$ 的密度分布, 可以指定`--atomic_mass` 选项, 如:
+```bash
+mdkits density [FILENAME] --element="name H" --cell [FILENAME] --atomic_mass=1.00784
+```
+则输出单位为 $g/cm^3$ 的密度分布. 可以指定表面原子来将密度分布归一化到表面, 如:
+```bash
+mdkits density [FILENAME] --element="name O" --cell 10,10,10 --atomic_mass=18.01528 --surface="name Pt and name Ru"
+```
+这样会将密度分布归一化到表面, 同时以O原子的位置作为水分子的位置分析处理水分子的密度分布. 对于体系中存在 $OH^-$ 离子的体系可以使用`--update_water`的选项在每一帧更新水分子的位置, 不需要额外指定元素, 如:
+```bash
+mdkits density [FILENAME] --update_water --cell 10,10,10 --atomic_mass=18.01528 --surface="name Pt and name Ru"
+```
+输出的文件名为`density_water.dat`.
 
 ### 氢键
 
@@ -77,7 +95,7 @@ mdkits convert -c structure.cif -o structure_xyz
 1. `--nor`: 对数据进行归一化处理
 2. `--gaus`: 对数据进行高斯过滤
 3. `--fold`: 堆数据进行折叠平均
-4. `--err`: 计算数据的误差棒
+4. `--err`: 计算数据的误差棒   
 等
 
 ### 绘图工具

{mdkits-0.1a4 → mdkits-0.1.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "mdkits"
-version = "0.1.a4"
+version = "0.1.1"
 description = "tools for md or dft"
 readme = "README.md"
 authors = ["jxxcr <jixxcr@qq.com>"]

mdkits-0.1.1/src/mdkits/cli/density.py

@@ -0,0 +1,134 @@
+#!/usr/bin/env python3
+
+import numpy as np
+import click
+from MDAnalysis import Universe
+from MDAnalysis.analysis.base import AnalysisBase
+from mdkits.util import (
+    arg_type,
+    numpy_geo,
+    encapsulated_mda,
+    os_operation,
+)
+import warnings, sys
+warnings.filterwarnings("ignore")
+
+
+class Density_distribution(AnalysisBase):
+    def __init__(self, filename, cell, o, element, atomic_mass, update_water, distance_judg, angle_judg, surface, dt=0.001, bin_size=0.2, return_index=False):
+        u = Universe(filename)
+        u.trajectory.ts.dt = dt
+        u.dimensions = cell
+
+        self.u = u
+        self.atomgroup = u.select_atoms("all")
+        self.bin_size = bin_size
+        self.frame_count = 0
+        self.return_index = return_index
+        self.surface = surface
+        self.atomic_mass = atomic_mass
+        self.update_water = update_water
+        self.element = element
+
+        if element is None and update_water is False:
+            sys.exit("Please specify the element to analysis or use --update-water option")
+
+        if self.update_water:
+            self.distance_judg = distance_judg
+            self.angle_judg = angle_judg
+
+        if o == 'density_{element}.dat':
+            if self.update_water:
+                self.o = "density_water.dat"
+            else:
+                self.o = f"density_{element.replace(' ', '_')}.dat"
+        else:
+            self.o = o
+
+        if surface is not None:
+            self.surface_group = self.atomgroup.select_atoms(f"{surface}")
+            if self.surface_group.n_atoms == 0:
+                sys.exit("Please specify the correct surface group")
+        else:
+            self.surface_group = False
+
+        super(Density_distribution, self).__init__(self.atomgroup.universe.trajectory, verbose=True)
+
+    def _prepare(self):
+        self.bin_num = int(self.u.dimensions[2] / self.bin_size) + 2
+        self.density_distribution = np.zeros(self.bin_num, dtype=np.float64)
+        if self.surface_group:
+            self.surface_pos = np.zeros(2)
+
+    def _append(self, z):
+        bins = np.floor(z / self.bin_size).astype(int) + 1
+        np.add.at(self.density_distribution, bins, 1)
+
+
+    def _single_frame(self):
+        if self.update_water:
+            o_group = self.atomgroup.select_atoms("name O")
+            h_group = self.atomgroup.select_atoms("name H")
+
+            o, oh1, oh2 = encapsulated_mda.update_water(self, o_group, h_group, distance_judg=self.distance_judg, angle_judg=self.angle_judg, return_index=self.return_index)
+
+            self._append(o.positions[:, 2])
+
+        else:
+            group = self.atomgroup.select_atoms(f"{self.element}")
+            self._append(group.positions[:, 2])
+
+        if self.surface_group:
+            lower_z, upper_z = numpy_geo.find_surface(self.surface_group.positions[:, 2], layer_tolerance=1, surface_tolerance=5)
+            self.surface_pos[0] += lower_z
+            self.surface_pos[1] += upper_z
+
+        self.frame_count += 1
+
+    def _conclude(self):
+        if self.frame_count > 0:
+            V = self.u.dimensions[0] * self.u.dimensions[1] * self.bin_size
+
+            if self.atomic_mass:
+                density_distribution = (self.density_distribution * self.atomic_mass * 1.660539 / V) / self.frame_count
+            else:
+                density_distribution = (self.density_distribution * (10000/6.02) / V) / self.frame_count
+
+            bins_z = np.arange(len(self.density_distribution)) * self.bin_size
+
+            if self.surface:
+                lower_z = self.surface_pos[0] / self.frame_count
+                upper_z = self.surface_pos[1] / self.frame_count
+
+                mask = (bins_z >= lower_z) & (bins_z <= upper_z)
+                filtered_bins_z = bins_z[mask] - lower_z
+                filtered_density_distribution = density_distribution[mask]
+
+                conbined_data = np.column_stack((filtered_bins_z, filtered_density_distribution))
+            else:
+                conbined_data = np.column_stack((bins_z, density_distribution))
+
+            np.savetxt(self.o, conbined_data, header="Z\tdensity", fmt='%.5f', delimiter='\t')
+
+@click.command(name='density')
+@click.argument('filename', type=click.Path(exists=True), default=os_operation.default_file_name('*-pos-1.xyz', last=True))
+@click.option('--cell', type=arg_type.Cell, help='set cell from cp2k input file or a list of lattice: --cell x,y,z or x,y,z,a,b,c', default='input.inp', show_default=True)
+@click.option('--element', type=str, help='element to analysis')
+@click.option('--atomic_mass', type=float, help='output density unit (g/cm3), should give atomic mass of element, else is concentration unit (mol/L)')
+@click.option('-o', type=str, help='output file name', default='density_{element}.dat', show_default=True)
+@click.option('--update_water', is_flag=True, help='update water with distance or angle judgment')
+@click.option('--distance', type=float, help='update water distance judgment', default=1.2, show_default=True)
+@click.option('--angle', type=(float, float), help='update water angle judgment')
+@click.option('--surface', type=str, help='surface element')
+def main(filename, cell, o, element, atomic_mass, update_water, distance, angle, surface):
+    """
+    analysis density or concentration of element in a trajectory file
+    """
+
+    density_dist = Density_distribution(filename, cell, o=o, distance_judg=distance, angle_judg=angle, element=element, atomic_mass=atomic_mass, update_water=update_water, surface=surface)
+
+    density_dist.run()
+
+
+if __name__ == '__main__':
+    main()

{mdkits-0.1a4 → mdkits-0.1.1}/src/mdkits/cli/plot.py

@@ -252,6 +252,10 @@ def mode_error(data_dict, figure, **kwargs):
 @click.option('--error', help='set error mode', is_flag=True)
 @click.option('-m', help='output mode: show, save, all, default is save', type=click.Choice(['show', 'save', 'all']), default='save')
 def main(yaml_file, int_ticks, error, m):
+    """
+    a plot tool, read yaml file to plot
+    """
+
     kwargs = locals()
     figure_dict = {}
     for yaml_file in yaml_file:

{mdkits-0.1a4 → mdkits-0.1.1}/src/mdkits/mdkits.py

@@ -5,6 +5,7 @@ from mdkits.cli import (
     extract,
     data,
     plot,
+    density
 )
 
 
@@ -12,7 +13,6 @@ from mdkits.cli import (
 @click.pass_context
 @click.version_option()
 def cli(ctx):
-    print(ctx)
     """tools for md or dft"""
     pass
 
@@ -22,6 +22,7 @@ cli.add_command(wrap.main)
 cli.add_command(extract.main)
 cli.add_command(data.main)
 cli.add_command(plot.main)
+cli.add_command(density.main)
 
 
 if __name__ == '__main__':

{mdkits-0.1a4 → mdkits-0.1.1}/src/mdkits/util/numpy_geo.py

@@ -97,7 +97,7 @@ def unwrap(atom1, atom2, coefficients, max=0, total=False):
 
 
 def find_surface(surface_group:np.ndarray, layer_tolerance=1, surface_tolerance=5):
-    sort_group = surface_group.sort()
+    sort_group = np.sort(surface_group)
     layer_mean = []
     current_layer = [sort_group[0]]
     for i in range(1, len(sort_group)):
@@ -106,6 +106,7 @@ def find_surface(surface_group:np.ndarray, layer_tolerance=1, surface_tolerance=
         else:
             layer_mean.append(np.mean(current_layer))
             current_layer = [sort_group[i]]
+        layer_mean.append(np.mean(current_layer))
     
     if len(current_layer) == 1:
         return layer_mean[0]
@@ -115,4 +116,4 @@ def find_surface(surface_group:np.ndarray, layer_tolerance=1, surface_tolerance=
         index = np.argmax(diff > 5)
         return (layer_mean[index], layer_mean[index + 1])
     else:
-        return layer_mean[-1]
+        return (layer_mean[-1], layer_mean[0])

mdkits-0.1a4/src/mdkits/cli/cmdline.py

@@ -1,41 +0,0 @@
-"""Command line"""
-import click
-from click import Context
-
-from mdkits import __version__
-from mdkits.config import settings
-from mdkits.log import init_log
-
-
-@click.group(invoke_without_command=True)
-@click.pass_context
-@click.option(
-    '-V',
-    '--version',
-    is_flag=True,
-    help='Show version and exit.'
-)  # If it's true, it will override `settings.VERBOSE`
-@click.option('-v', '--verbose', is_flag=True, help='Show more info.')
-@click.option(
-    '--debug',
-    is_flag=True,
-    help='Enable debug.'
-)  # If it's true, it will override `settings.DEBUG`
-def main(ctx: Context, version: str, verbose: bool, debug: bool):
-    """Main commands"""
-    if version:
-        click.echo(__version__)
-    elif ctx.invoked_subcommand is None:
-        click.echo(ctx.get_help())
-    else:
-        if verbose:
-            settings.set('VERBOSE', True)
-        if debug:
-            settings.set('DEBUG', True)
-
-
-@main.command()
-def run():
-    """Run command"""
-    init_log()
-    click.echo('run......')

mdkits-0.1a4/src/mdkits/cli/cp2k_input.py

@@ -1,479 +0,0 @@
-#!/usr/bin/env python3
-
-# is to generate cp2k input file 
-import argparse
-import shutil
-import os
-from ase.io import read, write
-from pymatgen.core.structure import Structure
-from pymatgen.io.cp2k.inputs import (
-	Cp2kInput, 
-	Section, 
-	Keyword, 
-	Cell, 
-	Coord, 
-	Kind
-)
-
-
-def insert_section(strs, section_name, section):
-
-	# to insert subsection to a high level section
-	insert = Cp2kInput.from_str(strs)
-	section.insert(insert.get_section(section_name))
-	
-	return section
-
-
-def add_keyword(keyword, section):
-
-	# to add keyword in a section
-	section.add(Keyword.from_str(keyword))
-
-
-def Global(
-	run_type="ENEGRY", 
-	project_name="cp2k", 
-	print_level="MEDIUM", 
-	walltime=107000
-):
-
-	# global section
-	Global = Section("GLOBAL")
-	
-	add_keyword(f"RUN_TYPE {run_type}", Global)
-	add_keyword(f"PROJECT_NAME {project_name}", Global)
-	add_keyword(f"PRINT_LEVEL {print_level}", Global)
-	add_keyword(f"WALLTIME {walltime}", Global)
-	
-	return Global
-
-
-def motion(
-	constraint_list=None,
-	cell_opt=False,
-	geo_opt=False
-):
-
-	# motion section
-	motion = Section("MOTION")
-	
-	## constraint subsection
-	if constraint_list != None:
-	    strs = f"""
-	    &CONSTRAINT
-	      &FIXED_ATOMS
-	        LIST {constraint_list}
-	      &END FIXED_ATOMS
-	    &END CONSTRAINT
-	    """
-	    insert_section(strs, "CONSTRAINT", motion)
-	
-	## cell_opt subsection
-	if cell_opt:
-	    strs = f"""
-	    &CELL_OPT
-	      OPTIMIZER BFGS
-	      MAX_ITER 200
-	    &END CELL_OPT
-	    """
-	    insert_section(strs, "CELL_OPT", motion)
-	
-	## geo_opt subsection
-	if geo_opt:
-	    strs = f"""
-	    &GEO_OPT
-	      TYPE MINIMIZATION
-	      OPTIMIZER BFGS
-	      MAX_ITER 500
-	    &END GEO_OPT
-	    """
-	    insert_section(strs, "GEO_OPT", motion)
-	
-	return motion
-
-
-def force_eval(
-	structure,
-	method="QUICKSTEP",
-	data_path="/public/software/cp2k-2022.1-intel/cp2k-2022.1/data",
-	charge=None,
-	ot=False,
-	hse=False
-):
-
-	# force_eval section
-	force_eval = Section("FORCE_EVAL")
-	add_keyword(f"METHOD {method}", force_eval)
-	
-	## dft subsection
-	dft = Section("DFT")
-	add_keyword(f"BASIS_SET_FILE_NAME {data_path}/BASIS_MOLOPT", dft)
-	add_keyword(f"POTENTIAL_FILE_NAME {data_path}/GTH_POTENTIALS", dft)
-	if isinstance(charge, int):
-	    dft.add_keyword(f"CHARGE {charge}", dft)
-	
-	### mgrid subsubsection
-	strs = """
-	&MGRID
-	  CUTOFF 400
-	&END MGRID
-	"""
-	insert_section(strs, "MGRID", dft)
-	
-	### qs subsubsection
-	strs = """
-	&QS
-	  EPS_DEFAULT 1.0E-13
-	  EXTRAPOLATION ASPC
-	  EXTRAPOLATION_ORDER 2
-	&END QS
-	"""
-	insert_section(strs, "QS", dft)
-	
-	### scf subsubsection
-	if ot:
-	    strs = """
-	    &SCF
-	      SCF_GUESS RESTART
-	      EPS_SCF 3.0E-6
-	      MAX_SCF 50
-	
-	      &OUTER_SCF
-	        EPS_SCF 3.0E-6
-	        MAX_SCF 20
-	      &END OUTER_SCF
-	
-	      &OT
-	        MINIMIZER DIIS
-	        PRECONDITIONER FULL_SINGLE_INVERSE
-	      &END OT
-	    &END SCF
-	    """
-	    insert_section(strs, dft)
-	else:
-	    strs = """
-	    &SCF
-	      SCF_GUESS RESTART
-	      EPS_SCF 3.0E-7
-	      MAX_SCF 500
-	      ADDED_MOS 500
-	      CHOLESKY INVERSE
-	
-	      &SMEAR ON
-	        METHOD FERMI_DIRAC
-	      &END SMEAR
-	
-	      &DIAGONALIZATION
-	        ALGORITHM STANDARD
-	      &END DIAGONALIZATION
-	
-	      &MIXING
-	        METHOD BROYDEN_MIXING
-	        ALPHA 0.15
-	        BETA 1.0
-	        NBROYDEN 16
-	      &END MIXING
-	
-	      &PRINT
-	
-	        &RESTART
-	          ADD_LAST NUMERIC
-	          
-	          &EACH
-	            QS_SCF 50
-	          &END EACH
-	        &END RESTART
-	      &END PRINT
-	    &END SCF
-	    """
-	    insert_section(strs, "SCF", dft)
-	
-	### xc subsubsection
-	if hse:
-	    strs = f"""
-	    &XC
-	
-	      &VDW_POTENTIAL
-	        DISPERSION_FUNCTIONAL PAIR_POTENTIAL
-	
-	        &PAIR_POTENTIAL
-	          TYPE DFTD3
-	          PARAMETER_FILE_NAME {data_path}/dftd3.dat
-	          REFERENCE_FUNCTIONAL PBE
-	        &END PAIR_POTENTIAL
-	      &END VDW_POTENTIAL
-	
-	      &XC_FUNCTIONAL
-	
-	        &XWPBE
-	          SCALE_X -0.25
-	          SCALE_X0 1.0
-	          OMEGA 0.11
-	        &END XWPBE
-	
-	        &PBE
-	          SCALE_X 0.0
-	          SCALE_C 1.0
-	        &END PBE
-	      &END XC_FUNCTIONAL
-	
-	      &HF
-	        FRACTION 0.25
-	
-	        &INTERACTION_POTENTIAL
-	          POTENTIAL_TYPE SHORTRANGE
-	          OMEGA 0.11
-	          T_C_G_DATA
-	        &END INTERACTION_POTENTIAL
-	
-	        &SCREENING
-	          EPS_SCHWARZ 1.0E-6
-	          SCREEN_ON_INITIAL_P .FALSE.
-	        &END SCREENING
-	
-	        &MEMORY
-	          MAX_MEMORY 3000
-	          EPS_STORAGE_SCALING 0.1
-	        &END MEMORY
-	
-	        &PERIODIC
-	          NUMPER_OF_SHELLS 0
-	        &END PERIODIC
-	      &END HF
-	    &END XC
-	    """
-	    insert_section(strs, "XC", dft)
-	else:
-	    strs = f"""
-	    &XC
-	
-	      &XC_FUNCTIONAL PBE
-	      &END XC_FUNCTIONAL
-	
-	      &VDW_POTENTIAL
-	        DISPERSION_FUNCTIONAL PAIR_POTENTIAL
-	
-	        &PAIR_POTENTIAL
-	          TYPE DFTD3
-	          PARAMETER_FILE_NAME {data_path}/dftd3.dat
-	          REFERENCE_FUNCTIONAL PBE
-	        &END PAIR_POTENTIAL
-	      &END VDW_POTENTIAL
-	    &END XC
-	    """
-	    insert_section(strs, "XC", dft)
-	
-	### print subsubsection
-	strs = """
-	&PRINT
-	
-	  &E_DENSITY_CUBE
-	    ADD_LAST NUMERIC
-	
-	    &EACH
-	      GEO_OPT 0
-	    &END EACH
-	  &END E_DENSITY_CUBE
-	
-	  &PDOS
-	    COMPONENTS .TRUE.
-	    NLUMO -1
-	    ADD_LAST NUMERIC
-	
-	    &EACH
-	      MD 50
-	      GEO_OPT 0
-	    &END EACH
-	  &END PDOS
-	
-	  &MO_CUBES
-	    NHOMO 5
-	    NLUMO 5
-	    WRITE_CUBE F
-	    ADD_LAST NUMERIC
-	    
-	    &EACH
-	      MD 50
-	      GEO_OPT 0
-	    &END EACH
-	  &END MO_CUBES
-	
-	  &V_HARTREE_CUBE ON
-	    STRIDE 8 8 1
-	    APPEND T
-	
-	    &EACH
-	      MD 50
-	      GEO_OPT 0
-	    &END EACH
-	  &END V_HARTREE_CUBE
-	&END PRINT
-	"""
-	insert_section(strs, "PRINT", dft)
-	
-	force_eval.insert(dft)
-	
-	## subsys subsection
-	subsys = Section("SUBSYS")
-	
-	### cell subsubsection
-	cell = Cell(structure.lattice)
-	subsys.insert(cell)
-
-	### coord subsubsection
-	coord = Section("COORD")
-	add_keyword("@INCLUDE ./coord.xyz", coord)
-	subsys.insert(coord)
-	
-	### kind subsubsection
-	for atom in structure.species:
-	    kind = Kind(atom, basis_set=None, potential=None)
-	    subsys.insert(kind)
-	
-	force_eval.insert(subsys)
-	
-	
-	return force_eval
-
-
-parser = argparse.ArgumentParser(description='generate cp2k input file')
-parser.add_argument('input_file_name', type=str, help='input file name')
-parser.add_argument('--cell', nargs="+", help='set cell, a list of lattice, [x, y, z] or [x, y, z, a, b, c]')
-parser.add_argument('--bp', type=str, nargs="?", default=None, help='a file contains all basis_set and potential information')
-## function args of golbal
-parser.add_argument('--run_type', type=str, nargs="?", default="ENEGRY", help='specie run_type keyword of global')
-parser.add_argument('--project_name', type=str, nargs="?", default="cp2k", help='specie project_name keyword of global')
-parser.add_argument('--print_level', type=str, nargs="?", default="MEDIUM", help='specie print_level keyword of global')
-parser.add_argument('--walltime', type=int, nargs="?", default=107000, help='specie walltime keyword of global')
-## function args of motion
-parser.add_argument('--constraint_list', type=str, nargs="?", default=None, help='specie constranit_list keyword of motion')
-parser.add_argument('--cell_opt', type=bool, nargs="?", default=False, help='specie cell_opt section of motion')
-parser.add_argument('--geo_opt', type=bool, nargs="?", default=False, help='specie geo_opt section of motion')
-## function args of force_eval
-parser.add_argument('--method', type=str, nargs="?", default="QUICKSTEP", help='specie methon keyword of force_eval')
-parser.add_argument('--charge', type=int, nargs="?", default=None, help='specie charge keyword of force_eval')
-parser.add_argument('--ot', type=bool, nargs="?", default=False, help='specie scf type is ot(else is smear) of force_eval')
-parser.add_argument('--hse', type=bool, nargs="?", default=False, help='specie xc type is hse(else is pbe) of force_eval')
-args = parser.parse_args()
-
-
-
-if args.input_file_name[-3:] == "xyz":
-	with open(args.input_file_name, 'r') as f:
-		data = f.readline().strip()
-		if not isinstance(int(data), int):
-			atom_number = sum(1 for line in f if line.strip)
-	
-			add_line = f"{int(atom_number+1)}\n\n"
-			with open(args.input_file_name, 'r') as g:
-				gile = g.readlines()
-				gile.insert(0, add_line)
-			with open(args.input_file_name, 'w') as g:
-				g.writelines(gile)
-
-if args.bp == None:
-	bp_dict = {
-		'Pt': ['DZVP-MOLOPT-SR-GTH', 'GTH-PBE-q18'], 
-		'O': ['DZVP-MOLOPT-SR-GTH', 'GTH-PBE-q6'], 
-		'C': ['DZVP-MOLOPT-SR-GTH', 'GTH-PBE-q4'],
-		'Cs': ['DZVP-MOLOPT-SR-GTH', 'GTH-PBE-q9'],
-		'Li': ['DZVP-MOLOPT-SR-GTH', 'GTH-PBE-q3'],
-		'Ne': ['DZVP-MOLOPT-SR-GTH', 'GTH-PBE-q8'], 
-		'Ru': ['DZVP-MOLOPT-SR-GTH', 'GTH-PBE-q16'], 
-		'Ag': ['DZVP-MOLOPT-SR-GTH', 'GTH-PBE-q11'], 
-		'Ir': ['DZVP-MOLOPT-SR-GTH', 'GTH-PBE-q17'], 
-		'C': ['DZVP-MOLOPT-SR-GTH', 'GTH-PBE-q4'], 
-		'H': ['DZVP-MOLOPT-SR-GTH', 'GTH-PBE-q1'], 
-		'F': ['DZVP-MOLOPT-SR-GTH', 'GTH-PBE-q7'], 
-		'Na': ['DZVP-MOLOPT-SR-GTH', 'GTH-PBE-q9'], 
-		'K': ['DZVP-MOLOPT-SR-GTH', 'GTH-PBE-q9'], 
-		'Cl': ['DZVP-MOLOPT-SR-GTH', 'GTH-PBE-q7']
-	}
-else:
-	bp_dict = {}
-	with open(args.bp, 'r') as f:
-		for line in f:
-			key, value1, value2 = line.strip().split()
-			bp_dict[key] = [value1, value2]
-
-
-if args.input_file_name[-3:] == "cif":
-	atoms = read(args.input_file_name)
-	atoms.write("POSCAR")
-	structure = Structure.from_file("POSCAR")
-	os.remove("POSCAR")
-
-elif args.input_file_name[-3:] == "xyz":
-	atoms = read(args.input_file_name, format="xyz")
-	atoms.set_cell(args.cell)
-	atoms.write("POSCAR", format="vasp")
-	structure = Structure.from_file("POSCAR")
-	os.remove("POSCAR")
-
-Global = Global(
-	run_type=args.run_type,
-	project_name=args.project_name,
-	print_level=args.print_level,
-	walltime=args.walltime
-)
-motion = motion(
-	constraint_list=args.constraint_list,
-	cell_opt=args.cell_opt,
-	geo_opt=args.geo_opt
-)
-force_eval = force_eval(
-	structure,
-	method=args.method,
-	charge=args.charge,
-	ot=args.ot,
-	hse=args.hse
-)
-
-used_bp_dict = {}
-for atom in structure.species:
-	if str(atom) in bp_dict:
-		used_bp_dict[str(atom)] = bp_dict[str(atom)]
-
-for key, value in used_bp_dict.items():
-	print(key, value)
-	add_keyword(f"BASIS_SET {value[0]}", force_eval.by_path(f"SUBSYS/{key}"))
-	add_keyword(f"POTENTIAL {value[1]}", force_eval.by_path(f"SUBSYS/{key}"))
-
-if args.input_file_name[-3:] == "cif":
-	atoms = read(args.input_file_name)
-	atoms.write("temp.xyz")
-	with open("temp.xyz", 'r') as f:
-		coord = ''
-		for i, line in enumerate(f):
-			if i < 2:
-				continue
-			coord += f"  {' '.join(line.split()[0:4])}\n"
-	
-	with open("coord.xyz", 'w') as f:
-		f.write(coord)
-	os.remove("temp.xyz")
-
-elif args.input_file_name[-3:] == "xyz":
-	with open(args.input_file_name, 'r') as f:
-		coord = ''
-		for i, line in enumerate(f):
-			if i < 2:
-				continue
-			coord += f"  {' '.join(line.split()[0:4])}\n"
-	
-	with open("coord.xyz", 'w') as f:
-		f.write(coord)
-		
-
-inp = Cp2kInput.from_str(
-	Global.get_str()+
-	motion.get_str()+
-	force_eval.get_str()
-)
-inp.write_file("input.inp")
-
-
-# copy sub script
-sub_script_path = "/public/home/jxxcr/script/sub_cp2k"
-shutil.copy2(sub_script_path, ".")

mdkits-0.1a4/src/mdkits/cli/density.py

@@ -1,89 +0,0 @@
-#!/usr/bin/env python3
-
-import numpy as np
-import click
-import MDAnalysis
-from MDAnalysis import Universe
-from MDAnalysis.analysis.base import AnalysisBase
-from mdkits.util import cp2k_input_parsing, numpy_geo, encapsulated_mda
-import warnings
-warnings.filterwarnings("ignore")
-
-
-class Density_distribution(AnalysisBase):
-    def __init__(self, filename, cell, o, distance_judg, angle_judg, dt=0.001, bin_size=0.2, return_index=False):
-        u = Universe(filename)
-        u.trajectory.ts.dt = dt
-        u.dimensions = cell
-
-        self.u = u
-        self.o = o
-        self.distance_judg = distance_judg
-        self.angle_judg = angle_judg
-        self.atomgroup = u.select_atoms("all")
-        self.mid_z = u.dimensions[2]/2
-        self.bin_size = bin_size
-        self.frame_count = 0
-        self.return_index = return_index
-
-        super(Density_distribution, self).__init__(self.atomgroup.universe.trajectory, verbose=True)
-
-    def _prepare(self):
-        self.bin_num = int(self.u.dimensions[2] / self.bin_size) + 2
-        self.density_distribution = np.zeros(self.bin_num, dtype=np.float64)
-        if self.surface:
-            self.surface_pos = ()
-
-    def _append(self, z):
-        bins = np.floor(z / self.bin_size).astype(int) + 1
-        np.add.at(self.density_distribution, bins, 1)
-
-    def _single_frame(self):
-        if self.water:
-            o_group = self.atomgroup.select_atoms("name O")
-            h_group = self.atomgroup.select_atoms("name H")
-
-            o, oh1, oh2 = encapsulated_mda.update_water(self, o_group, h_group, distance_judg=self.distance_judg, angle_judg=self.angle_judg, return_index=self.return_index)
-
-            self._append(o.positions[:, 2])
-
-        else:
-            group = self.atomgroup.select_atoms(f"name {self.element}")
-            self._append(group.positions[:, 2])
-
-        self.
-        self.frame_count += 1
-
-    def _conclude(self):
-        if self.frame_count > 0:
-            V = self.u.dimensions[0] * self.u.dimensions[1] * self.bin_size
-
-            if self.water:
-                density_distribution = (self.density_distribution * (15.999+1.008*2) * 1.660539 / V) / self.frame_count
-            else:
-                density_distribution = (self.density_distribution * (10000/6.02) / V) / self.frame_count
-
-            bins_z = np.arange(len(self.density_distribution)) * self.bin_size
-
-            surface = self.find_surface(self.atomgroup.select_atoms("name Pt"))
-
-            lower_z, upper_z = surface
-            mask = (bins_z >= lower_z) & (bins_z <= upper_z)
-            filtered_bins_z = bins_z[mask] - lower_z
-            filtered_density_distribution = density_distribution[mask]
-            conbined_data = np.column_stack((filtered_bins_z, filtered_density_distribution))
-
-            np.savetxt(self.o, conbined_data, header="Z\tdensity", fmt='%.5f', delimiter='\t')
-
-@click.command(name='density')
-@click.argument('filename', type=click.Path(exists=True), default=os_operation.default_file_name('*-pos-1.xyz', last=True))
-@click.option('--cell', type=arg_type.Cell, help='set xyz file cell, --cell x,y,z,a,b,c')
-@click.option('--cell', type=arg_type.Cell, help='set cell from cp2k input file or a list of lattice: --cell x,y,z or x,y,z,a,b,c', default='input.inp', show_default=True)
-@click.option('-o', type=str, help='output file name', default='density.dat', show_default=True)
-def main(filename, cell, o):
-    density_dist = Density_distribution(filename, cell, o=o)
-    density_dist.run()
-
-
-if __name__ == '__main__':
-    main()

mdkits-0.1a4/src/mdkits/cli/density2.py

@@ -1,91 +0,0 @@
-#!/usr/bin/env python3
-
-import os, sys, argparse
-import numpy as np
-import math
-import multiprocessing
-from util import (
-    structure_parsing,
-    cp2k_input_parsing,
-    os_operation,
-    atom_count,
-    )
-
-
-def array_type(string):
-	number_list = string.split(',')
-	number_array = array(number_list, dtype=float)
-	return number_array
-
-
-def get_cell(cp2k_input_file, cell=None):
-    if cell is None:
-        cell = cp2k_input_parsing.parse_cell(cp2k_input_file)
-    else:
-        cell = cell
-        if len(cell) == 3:
-            cell.extend([90.0, 90.0, 90.0])
-
-    return cell
-
-
-def parse_cell(s):
-    if s == None:
-        return None
-    return [float(x) for x in s.replace(',', ' ').split()]
-
-
-# set argument
-def parse_argument():
-    parser = argparse.ArgumentParser(description='calculate water density destribution alone z axis')
-
-    parser.add_argument('input_file_name', type=str, nargs='?', help='input file name', default=os_operation.default_file_name('*-pos-1.xyz', last=True))
-    #parser.add_argument('-a', type=str, help='atom to statistic', default='O')
-    parser.add_argument('-o', type=str, help='output file name, default is "density.dat"', default='density.dat')
-    parser.add_argument('-r', type=array_type, help='bulk range')
-    parser.add_argument('--cp2k_input_file', type=str, help='input file name of cp2k, default is "input.inp"', default='input.inp')
-    parser.add_argument('--cell', type=parse_cell, help='set cell, a list of lattice, [x,y,z] or [x,y,z,a,b,c]')
-    parser.add_argument('--process', type=int, help='paralle process number default is 28', default=28)
-    parser.add_argument('--temp', help='keep temp file', action='store_false')
-
-    return parser.parse_args()
-
-
-def main():
-    args = parse_argument()
-    bin_size = 0.2
-    cell = get_cell(args.cp2k_input_file, args.cell)
-    temp_dir = f'{os.environ.get("TEMP_DIR")}/{os.getpid()}'
-    os_operation.make_temp_dir(temp_dir, delete=args.temp)
-    chunks = structure_parsing.xyz_to_chunks(args.input_file_name, args.process)
-    group = structure_parsing.chunk_to_groups(chunks[0])[0]
-    atom_names = structure_parsing.atom_name_parse(group)
-    for atom_name in atom_names:
-        for index, chunk in enumerate(chunks):
-            t = multiprocessing.Process(target=atom_count.atom_number_count, args=[chunk, bin_size, cell[2], atom_name, f'{temp_dir}/chunk_{index}.temp'])
-            t.start()
-
-        for t in multiprocessing.active_children():
-            t.join()
-
-        chunks_array_list = []
-        for i in range(len(chunks)):
-            chunk_array = np.load(f'{temp_dir}/chunk_{i}.temp.npy')
-            chunks_array_list.append(chunk_array)
-        chunks_array = np.vstack(chunks_array_list)
-        chunks_array = np.mean(chunks_array, axis=0)
-        if atom_name == 'O':
-            chunks_array = chunks_array * (15.999+1.0080*2) * 1.660539 / (cell[0]*cell[1]*bin_size)
-            with open(f'density_water.dat', 'w') as f:
-                for i in range(len(chunks_array)):
-                    f.write(str((i+1)*bin_size) + '\t' + str(chunks_array[i]) + '\n')
-
-        chunks_array = chunks_array * (10000/6.02) / (cell[0]*cell[1]*bin_size)
-        with open(f'density_{atom_name}.dat', 'w') as f:
-            for i in range(len(chunks_array)):
-                f.write(str((i+1)*bin_size) + '\t' + str(chunks_array[i]) + '\n')
-
-        print(f"density analysis of {atom_name} is done")
-
-if __name__ == '__main__':
-    main()

mdkits-0.1a4/src/mdkits/cli/log.py

@@ -1,64 +0,0 @@
-"""Log"""
-import logging
-import os
-from logging.config import dictConfig
-
-from mdkits.config import settings
-
-os.makedirs(settings.LOGPATH, exist_ok=True)
-
-
-def verbose_formatter(verbose: int) -> str:
-    """formatter factory"""
-    if verbose is True:
-        return 'verbose'
-    return 'simple'
-
-
-def update_log_level(debug: bool, level: str) -> str:
-    """update log level"""
-    if debug is True:
-        level_num = logging.DEBUG
-    else:
-        level_num = logging.getLevelName(level)
-    settings.set('LOGLEVEL', logging.getLevelName(level_num))
-    return settings.LOGLEVEL
-
-
-def init_log() -> None:
-    """Init log config."""
-    log_level = update_log_level(settings.DEBUG, str(settings.LOGLEVEL).upper())
-
-    log_config = {
-        "version": 1,
-        "disable_existing_loggers": False,
-        "formatters": {
-            'verbose': {
-                'format': '%(asctime)s %(levelname)s %(name)s %(process)d %(thread)d %(message)s',
-            },
-            'simple': {
-                'format': '%(asctime)s %(levelname)s %(name)s %(message)s',
-            },
-        },
-        "handlers": {
-            "console": {
-                "formatter": verbose_formatter(settings.VERBOSE),
-                'level': 'DEBUG',
-                "class": "logging.StreamHandler",
-            },
-            'file': {
-                'class': 'logging.handlers.RotatingFileHandler',
-                'level': 'DEBUG',
-                'formatter': verbose_formatter(settings.VERBOSE),
-                'filename': os.path.join(settings.LOGPATH, 'all.log'),
-                'maxBytes': 1024 * 1024 * 1024 * 200,  # 200M
-                'backupCount': '5',
-                'encoding': 'utf-8'
-            },
-        },
-        "loggers": {
-            '': {'level': log_level, 'handlers': ['console']},
-        }
-    }
-
-    dictConfig(log_config)

mdkits-0.1a4/src/mdkits/cli/matplot.py

@@ -1,60 +0,0 @@
-#!/usr/bin/env python3
-
-import numpy as np
-import matplotlib.pyplot as plt
-import argparse
-import os
-from matplotlib import use as muse
-muse('Agg')
-
-
-def parse_slice(s):
-    if s == None:
-        return None
-    return [int(x) for x in s.replace(':', ' ').split()]
-
-
-def parse_argument():
-    parser = argparse.ArgumentParser(description='extract pos file from output file')
-
-    parser.add_argument('input_file_name', type=str, help='input file name')
-    parser.add_argument('-o', type=str, help='output file name, default is "out.xyz"', default='out.png')
-    parser.add_argument('-u', type=parse_slice, help='which clume to use, look like gnuplot u 1:2', default=[0, 1])
-    parser.add_argument('--label', type=str, help='line name')
-    parser.add_argument('--dpi', type=int, help='image dpi, default is 300', default=300)
-    parser.add_argument('--err',  help='plot err line', action='store_true')
-
-    return parser.parse_args()
-
-
-def plot_data(x, y, dpi, label, name):
-    fig, ax = plt.subplots(dpi=dpi)
-    ax.plot(x, y, label=label)
-    ax.legend()
-    fig.savefig(name)
-
-
-def plot_err(x, y, dpi, label, name):
-    fig, ax = plt.subplots(dpi=dpi)
-    ax.scatter(x, y, label=label)
-    line = np.linspace(np.amax(x), np.amin(x), 1000)
-    ax.plot(line, line)
-    ax.legend()
-    fig.savefig(name)
-
-
-def main():
-    args = parse_argument()
-    if args.label == None:
-        args.label = args.input_file_name
-    data = np.loadtxt(args.input_file_name)
-    if args.err:
-        plot_err(data[:, 0], data[:, 1], dpi=args.dpi, label=args.label, name=args.o)
-    else:
-        plot_data(data[:, 0], data[:, 1], dpi=args.dpi, label=args.label, name=args.o)
-
-    print(os.path.abspath(args.o))
-
-
-if __name__ == '__main__':
-    main()