mdkits 0.1.3__py3-none-any.whl → 0.1.4__py3-none-any.whl

mdkits/cli/build_bulk.py

@@ -1,53 +1,33 @@
 #!/usr/bin/env python3
 
-import argparse
+import click
 from ase.build import bulk
-from ase.geometry import cell_to_cellpar
-from ase.io import write
-
-
-def parse_size(s):
-    return [int(x) for x in s.replace(',', ' ').split()]
-
-
-def parse_argument():
-    parser = argparse.ArgumentParser(description='build a surface structure of matel')
-    parser.add_argument('symbol', type=str, help='designate the symbol of matel')
-    parser.add_argument('--crystal', type=str, help='designate the crystal of structure')
-    parser.add_argument('--orth', help='outpue orthorhombic crystal', action='store_true')
-    parser.add_argument('-a', type=float, help='designate a lattice constant')
-    parser.add_argument('--primitve', help='designate a lattice constant of real', action='store_true')
-    parser.add_argument('-o', type=str, help='output structure name', default='bulk.xyz')
-    parser.add_argument('-c', help='output coord.xyz and cell.inc', action='store_true')
-    parser.add_argument('-k', help='output kpoint.inc', action='store_true')
-
-    return parser.parse_args()
-
-
-def main():
-    args = parse_argument()
-    if args.primitve:
-        a = args.a * 0.7071 * 2
-    else:
-        a = args.a
-    atoms = bulk(args.symbol, args.crystal, a=a, orthorhombic=args.orth)
-    if args.c:
-        atoms.write('coord.xyz', format='xyz')
-        with open('coord.xyz', 'r') as f:
-            lines = f.readlines()[2:]
-        with open('coord.xyz', 'w') as f:
-            f.writelines(lines)
-        with open('cell.inc', 'w') as f:
-            cell = list(cell_to_cellpar(atoms.cell))
-            f.write('ABC [angstrom] ' + str(cell[0]) + ' ' + str(cell[1]) + ' ' + str(cell[2]) + ' ' + '\n')
-            f.write('ALPHA_BETA_GAMMA ' + str(cell[3]) + ' ' + str(cell[4]) + ' ' + str(cell[5]) + '\n')
-        if args.k:
-            with open('kpoint.inc', 'w') as f:
-                if True:
-                    if True:
-                        f.write(f"SCHEME MONKHORST-PACK {int(round(30/cell[0]))} {int(round(30/cell[1]))} {int(round(30/cell[2]))}" + "\n")
-    else:
-        atoms.write(args.o)
+import numpy as np
+
+
+@click.command(name='build_bulk')
+@click.argument('symbol', type=str)
+@click.argument('cs', type=click.Choice(['sc', 'fcc', 'bcc', 'tetragonal', 'bct', 'hcp', 'rhombohedral', 'orthorhombic', 'mcl', 'diamond', 'zincblende', 'rocksalt', 'cesiumchloride', 'fluorite', 'wurtzite']))
+@click.option('-a', type=float, help='designate lattice constant a')
+@click.option('-b', type=float, help='designate lattice constant b. if only a and b is given, b will be interpreted as c instead')
+@click.option('-c', type=float, help='designate lattice constant c')
+@click.option('--alpha', type=float, help='angle in degrees for rhombohedral lattice')
+@click.option('--covera', type=float, help='c/a ratio used for hcp. Default is ideal ratio: sqrt(8/3)', default=np.sqrt(8/3), show_default=True)
+@click.option('-u', type=float, help='internal coordinate for Wurtzite structure')
+@click.option('--orth', is_flag=True, help='construct orthorhombic unit cell instead of primitive cell which is the default')
+@click.option('--cubic', is_flag=True, help='construct cubic unit cell if possible')
+def main(symbol, cs, a, b, c, alpha, covera, u, orth, cubic):
+    """
+    build a bulk structure
+    """
+
+    #if args.primitve:
+    #    a = args.a * 0.7071 * 2
+    #else:
+    #    a = args.a
+    atoms = bulk(symbol, cs, a=a, b=b, c=c, alpha=alpha, covera=covera, u=u, orthorhombic=orth, cubic=cubic)
+
+    atoms.write(f"{symbol}_{cs}.cif", format='cif')
 
 
 if __name__ == '__main__':

mdkits/mdkits.py

@@ -8,6 +8,7 @@ from mdkits.cli import (
     density,
     cube,
     pdos,
+    build_bulk,
 )
 
 
@@ -27,6 +28,7 @@ cli.add_command(plot.main)
 cli.add_command(density.main)
 cli.add_command(cube.main)
 cli.add_command(pdos.main)
+cli.add_command(build_bulk.main)
 
 
 if __name__ == '__main__':

{mdkits-0.1.3.dist-info → mdkits-0.1.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 0.1.3
+Version: 0.1.4
 Summary: tools for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory
@@ -97,6 +97,25 @@ mdkits cube [FILENAME] -b 1 2
 ```
 会将平均值打印在屏幕上, 同时记录在`cube.out`中的注释行.
 
+## 建模
+### 构建体相模型
+`build_bulk`用于构建体相模型, 如构建`Pt`的`fcc`体相模型:
+```bash
+mdkits build_bulk Pt fcc
+```
+构建为常胞模型:
+```bash
+mdkits build_bulk Pt fcc --cubic
+```
+构建一个`Caesium chloride`结构的模型:
+```bash
+mdkits build_bulk CsCl cesiumchloride -a 4.123
+```
+构建一个`fluorite `结构的模型:
+```bash
+mdkits build_bulk BaF2 fluorite -a 6.196
+```
+
 ## 其他
 ### 轨迹提取
 `extract`用于提取轨迹文件中的特定的帧, 如从`frames.xyz`中提取第 1000 帧到第 2000 帧的轨迹文件, 并输出为`1000-2000.xyz`, `-r`选项的参数与`Python`的切片语法一致:

{mdkits-0.1.3.dist-info → mdkits-0.1.4.dist-info}/RECORD

@@ -1,7 +1,7 @@
 mdkits/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 "mdkits/cli/,hb_distribution_down.py",sha256=i3NguzGebqCgy4uuVBeFajZRZnXtjhsJBPDGDdumlWA,4733
 mdkits/cli/adsorbate.py,sha256=6PN6qVSzhOFLxjUal4T2Qk5W5XUWAUn5-JXS8-D0xqo,3126
-mdkits/cli/build_bulk.py,sha256=dto5Wj-RcpzaGvyqTamo-3UfjQFQ_6cjy5_lMG0grPk,2117
+mdkits/cli/build_bulk.py,sha256=LJwC7IqDV_dY2cJJHwk9stqLu3wzbXxC87GMbyaalw0,1555
 mdkits/cli/build_interface.py,sha256=i1YE5iwazKVsTdQ_DXalNYeA8oflORWFePgJin1AJM4,3537
 mdkits/cli/build_surface.py,sha256=tL9rSv6MROPRtVUu8JiPJbt4YdHFVKTZrEUaSd3rlzI,5657
 mdkits/cli/convert.py,sha256=s2q2Py7IVGNTctHgpHm66YFj_Rr8srnpuJudrMBI0oM,2014
@@ -21,7 +21,7 @@ mdkits/cli/supercell.py,sha256=r5iddLw1NNzj7NTFlR2j_jpD1AMfrsxhA08bPwQvVvg,2059
 mdkits/cli/wrap.py,sha256=AUxGISuiCfEjdMYl-TKc2VMCPHSybWKrMIOTn_6kSp0,1043
 mdkits/config/__init__.py,sha256=ZSwmnPK02LxJLMgcYmNb-tIOk8fEuHf5jpqD3SDHWLg,1039
 mdkits/config/settings.yml,sha256=PY7u0PbFLuxSnd54H5tI9oMjUf-mzyADqSZtm99BwG0,71
-mdkits/mdkits.py,sha256=S4aVIxiS9tcuuELSTGpXlZtOsNhLNyc31uzLV_pEyeE,550
+mdkits/mdkits.py,sha256=cItenwSa9YWtd-YGg49l52VoIBDWqqeZmPIdx6LcqU0,601
 mdkits/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mdkits/util/arg_type.py,sha256=YUFhYShTYfUe7xajgUCiCuaeNLH-wxMXvlcMRax4zRM,1469
 mdkits/util/cp2k_input_parsing.py,sha256=6BFVsbBYxdauaUPrjr5h8JXk_R0bu7V3cbG2DEWWFlQ,1291
@@ -31,8 +31,8 @@ mdkits/util/fig_operation.py,sha256=FwffNUtXorMl6qE04FipgzcVljEQii7wrNJUCJMyY3E,
 mdkits/util/numpy_geo.py,sha256=1Op8THoQeyqybSZAi7hVxohYCr4SzY6ndZC8_gAGXDA,3619
 mdkits/util/os_operation.py,sha256=tNRjniDwFqARMy5Rf6MUNmaQGpJlyifCpuN16r8aB2g,828
 mdkits/util/structure_parsing.py,sha256=mRPMJeih3O-ST7HeETDvBEkfV-1psT-XgxyYgDadV0U,4152
-mdkits-0.1.3.dist-info/entry_points.txt,sha256=xoWWZ_yL87S501AzCO2ZjpnVuYkElC6z-8J3tmuIGXQ,44
-mdkits-0.1.3.dist-info/LICENSE,sha256=VLaqyB0r_H7y3hUntfpPWcE3OATTedHWI983htLftcQ,1081
-mdkits-0.1.3.dist-info/METADATA,sha256=FeNoHay-d-Lp8q4_b_LaifawnqxesqgeZBlnVvEqHEA,6074
-mdkits-0.1.3.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
-mdkits-0.1.3.dist-info/RECORD,,
+mdkits-0.1.4.dist-info/entry_points.txt,sha256=xoWWZ_yL87S501AzCO2ZjpnVuYkElC6z-8J3tmuIGXQ,44
+mdkits-0.1.4.dist-info/LICENSE,sha256=VLaqyB0r_H7y3hUntfpPWcE3OATTedHWI983htLftcQ,1081
+mdkits-0.1.4.dist-info/METADATA,sha256=i_qFaaji3Kb0FL8KGYaQPLHuhPhskcTM9pizTqIfeTE,6485
+mdkits-0.1.4.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
+mdkits-0.1.4.dist-info/RECORD,,