mdkits 0.1a2__py3-none-any.whl → 0.1a4__py3-none-any.whl

mdkits/cli/cmdline.py

@@ -2,9 +2,9 @@
 import click
 from click import Context
 
-from mdtool import __version__
-from mdtool.config import settings
-from mdtool.log import init_log
+from mdkits import __version__
+from mdkits.config import settings
+from mdkits.log import init_log
 
 
 @click.group(invoke_without_command=True)

mdkits/cli/convert.py

@@ -3,7 +3,7 @@
 from ase.io import write
 import click
 import os
-from mdtool.util import encapsulated_ase, arg_type
+from mdkits.util import encapsulated_ase, arg_type
 
 
 @click.command(name='convert')

mdkits/cli/density.py

@@ -5,7 +5,7 @@ import click
 import MDAnalysis
 from MDAnalysis import Universe
 from MDAnalysis.analysis.base import AnalysisBase
-from mdtool.util import cp2k_input_parsing, numpy_geo, encapsulated_mda
+from mdkits.util import cp2k_input_parsing, numpy_geo, encapsulated_mda
 import warnings
 warnings.filterwarnings("ignore")
 

mdkits/cli/extract.py

@@ -4,7 +4,7 @@
 
 import os
 import click
-from mdtool.util import os_operation, arg_type
+from mdkits.util import os_operation, arg_type
 import MDAnalysis
 from MDAnalysis import Universe
 

mdkits/cli/log.py

@@ -3,7 +3,7 @@ import logging
 import os
 from logging.config import dictConfig
 
-from mdtool.config import settings
+from mdkits.config import settings
 
 os.makedirs(settings.LOGPATH, exist_ok=True)
 

mdkits/cli/plot.py

@@ -6,7 +6,7 @@ from matplotlib import pyplot as plt
 from matplotlib import rcParams
 import matplotlib.ticker as ticker
 import yaml, click
-from mdtool.util import fig_operation
+from mdkits.util import fig_operation
 
 DEFAULT_CONFIG = {
         'data': {},

mdkits/cli/wrap.py

@@ -3,7 +3,7 @@
 import os
 from MDAnalysis import Universe
 import MDAnalysis, click
-from mdtool.util import (
+from mdkits.util import (
     arg_type,
     os_operation,
     cp2k_input_parsing

mdkits/config/__init__.py

@@ -18,17 +18,17 @@ _settings_files = [
 
 # User configuration. It will be created automatically by the pip installer .
 _external_files = [
-    Path(sys.prefix, 'etc', 'mdtool', 'settings.yml')
+    Path(sys.prefix, 'etc', 'mdkits', 'settings.yml')
 ]
 
 
 settings = Dynaconf(
-    # Set env `MDTOOL_FOO='bar'`，use `settings.FOO` .
-    envvar_prefix='MDTOOL',
+    # Set env `mdkits_FOO='bar'`，use `settings.FOO` .
+    envvar_prefix='mdkits',
     settings_files=_settings_files,  # load user configuration.
     # environments=True,  # Enable multi-level configuration，eg: default, development, production
     load_dotenv=True,  # Enable load .env
-    # env_switcher='MDTOOL_ENV',
+    # env_switcher='mdkits_ENV',
     lowercase_read=False,  # If true, can't use `settings.foo`, but can only use `settings.FOO`
     includes=_external_files,  # Customs settings.
     base_dir=_base_dir,  # `settings.BASE_DIR`

mdkits/config/settings.yml

@@ -1,4 +1,4 @@
 verbose: false
 debug: false
 loglevel: warning
-logpath: /tmp/mdtool
+logpath: /tmp/mdkits

mdkits/mdkits.py

@@ -1,5 +1,5 @@
 import click
-from mdtool.cli import (
+from mdkits.cli import (
     convert,
     wrap,
     extract,

{mdkits-0.1a2.dist-info → mdkits-0.1a4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 0.1a2
+Version: 0.1a4
 Summary: tools for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory
@@ -24,9 +24,9 @@ Project-URL: Repository, https://github.com/jxxcr/mdkits
 Description-Content-Type: text/markdown
 
 # MD 轨迹分析脚本
-`mdtool` 提供了多种工具, 安装脚本:
+`mdkits` 提供了多种工具, 安装脚本:
 ```bash
-pip install mdtool --upgrade
+pip install mdkits --upgrade
 ```
 ### 密度分布
 
@@ -49,15 +49,15 @@ pip install mdtool --upgrade
 ### 位置归一化
 `wrap`用于将轨迹文件中的原子位置进行归一化处理, 如将`[FILENAME]`中的原子位置归一化到晶胞中, 并输出为`wrapped.xyz`, 默认从`cp2k`的输出文件`input_inp`中读取`ABC`和`ALPHA_BETA_GAMMA`信息作为晶胞参数:
 ```bash
-mdtool wrap [FILENAME] 
+mdkits wrap [FILENAME] 
 ```
 或指定`cp2k`的输入文件:
 ```bash
-mdtool wrap [FILENAME] --cp2k_input_file setting.inp
+mdkits wrap [FILENAME] --cp2k_input_file setting.inp
 ```
 或指定晶胞参数:
 ```bash
-mdtool wrap [FILENAME] --cell 10,10,10
+mdkits wrap [FILENAME] --cell 10,10,10
 ```
 默认的`[FILENAME]`为`*-pos-1.xyz`
 
@@ -72,29 +72,29 @@ mdtool wrap [FILENAME] --cell 10,10,10
 ### 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:
 ```bash
-mdtool extract frames.xyz -r 1000:2000 -o 1000-2000.xyz
+mdkits extract frames.xyz -r 1000:2000 -o 1000-2000.xyz
 ```
 或从`cp2k`的默认输出的轨迹文件`*-pos-1.xyz`文件中提取最后一帧输出为`extracted.xyz`(`extract`的默认行为):
 ```bash
-mdtool extract
+mdkits extract
 ```
 或每50帧输出一个结构到`./coord`目录中, 同时调整输出格式为`cp2k`的`@INCLUDE coord.xyz`的形式:
 ```bash
-mdtool extract -cr ::50
+mdkits extract -cr ::50
 ```
 
 ### 结构文件转换
 `convert`用于将结构文件从一种格式转换为另一种格式, 如将`structure.xyz`转换为`out.cif`(默认文件名为`out`), 对于不储存周期性边界条件的文件, 可以使用`--cell`选项指定`PBC`:
 ```bash
-mdtool convert -c structure.xyz --cell 10,10,10
+mdkits convert -c structure.xyz --cell 10,10,10
 ```
 将`structure.cif`转换为`POSCAR`:
 ```bash
-mdtool convert -v structure.cif
+mdkits convert -v structure.cif
 ```
 将`structure.cif`转换为`structure_xyz.xyz`:
 ```bash
-mdtool convert -c structure.cif -o structure_xyz
+mdkits convert -c structure.cif -o structure_xyz
 ```
 
 ### 数据处理
@@ -153,9 +153,9 @@ figure2:
 
 `plot`可以同时处理多个`yaml`文件, 每个`yaml`文件可以包含多个绘图配置, `mode 1`和`mode 2`的绘图配置可以自动识别, 但是`error`模式需要而外指定, 如:
 ```bash
-mdtool plot *.yaml
+mdkits plot *.yaml
 ```
 和:
 ```bash
-mdtool plot *.yaml --error
+mdkits plot *.yaml --error
 ```

{mdkits-0.1a2.dist-info → mdkits-0.1a4.dist-info}/RECORD

@@ -5,28 +5,28 @@ mdkits/cli/adsorbate.py,sha256=6PN6qVSzhOFLxjUal4T2Qk5W5XUWAUn5-JXS8-D0xqo,3126
 mdkits/cli/build_bulk.py,sha256=dto5Wj-RcpzaGvyqTamo-3UfjQFQ_6cjy5_lMG0grPk,2117
 mdkits/cli/build_interface.py,sha256=i1YE5iwazKVsTdQ_DXalNYeA8oflORWFePgJin1AJM4,3537
 mdkits/cli/build_surface.py,sha256=tL9rSv6MROPRtVUu8JiPJbt4YdHFVKTZrEUaSd3rlzI,5657
-mdkits/cli/cmdline.py,sha256=ybTNLCcbOSKTiDkhf6lorV_TL4ogRB2c_q8QoUbw7bg,1046
-mdkits/cli/convert.py,sha256=McwSTs_rhe2a096r6Hc5DkMTS8OjEfg61W5A5afgeX4,2014
+mdkits/cli/cmdline.py,sha256=bARlAxI-F_iLVwuWCADkCCPusRiJID0rmOK84pumi0E,1046
+mdkits/cli/convert.py,sha256=s2q2Py7IVGNTctHgpHm66YFj_Rr8srnpuJudrMBI0oM,2014
 mdkits/cli/cp2k_input.py,sha256=EskBUSaAOLmrrUYGruTwZjEy9EksdEhWwR5ys9juIbg,11139
 mdkits/cli/cube.py,sha256=XcJfsJ5Y2d5MQfD45p06_gV1fTJbDSrNhCnZ3Sz2Vb0,2233
 mdkits/cli/cut_surface.py,sha256=D1naCWj0QJE3AiInzy3SeGO37butothE3BS1rZsZ5MU,1425
 mdkits/cli/data.py,sha256=FGA4S9Cfo6WUJBSPWKOJrrZXHo_Qza-jNG1P_Dw7yi4,3262
-mdkits/cli/density.py,sha256=t8d5lxkmUtrIrxy5B2_OK3qtTUS5nTTalJ2dgJh-vVY,3530
+mdkits/cli/density.py,sha256=ISn1MMfFHmw4sPTSF8B5f-e1rZohyBWxjnpQU53pxgk,3530
 mdkits/cli/density2.py,sha256=I1OtC7s979Ks7GOH47hTKUGE1h6tUFYvNZQ7Qbifs6I,3458
-mdkits/cli/extract.py,sha256=4QI78Zx9wtiEQk3FegMOFikMSJvfBCBikeZp121WrF8,2498
+mdkits/cli/extract.py,sha256=bqqJBmSaVyPYyEseGpUJcMBufIfDLTNRdmUfJ0txE5E,2498
 mdkits/cli/hartree_potential.py,sha256=XcJfsJ5Y2d5MQfD45p06_gV1fTJbDSrNhCnZ3Sz2Vb0,2233
 mdkits/cli/hartree_potential_ave.py,sha256=25oy3QsgIdxrTFpTqpnGvLAheb-d6poeLMN7iuGT3Xk,3335
 mdkits/cli/hb.py,sha256=lADr4tlctbtQ3_f_UpznkLnSI0MJlAT-pknEf_dwrnU,5330
-mdkits/cli/log.py,sha256=2WD0AimvAezqCFTmMLkXR_Gr2Rh5KRb47IzYOVcXcqY,1916
+mdkits/cli/log.py,sha256=vObagvnQhD_ttfuWPGqyubF-ssCHk-hxfx30lM95qhU,1916
 mdkits/cli/matplot.py,sha256=j6Z9vynNd8qPA_QzXDpQ-3pxLk7woRsFJep8W5iNm-E,1739
 mdkits/cli/packmol_input.py,sha256=76MjjMMRDaW2q459B5mEpXDYSSn14W-JXudOOsx-8E4,2849
 mdkits/cli/pdos.py,sha256=wkv4TD02fHKR0gDQ_h738Iu8_0xPKBOesVdngVZ-YfI,1044
-mdkits/cli/plot.py,sha256=bWUj4Cvz8fHn_FcdZ3C3rUDd5LNO97Qvc5UVNq6UdOc,8881
+mdkits/cli/plot.py,sha256=yOimB2YzcsJkLl1_dJhec3Q0RkEprvjQtB_yz4Dmaqo,8881
 mdkits/cli/supercell.py,sha256=r5iddLw1NNzj7NTFlR2j_jpD1AMfrsxhA08bPwQvVvg,2059
-mdkits/cli/wrap.py,sha256=ZKJu0zG7z9mVG2n3RDX3fy0FTqQhOnHmUvA90hLhWX8,1043
-mdkits/config/__init__.py,sha256=t3fgtnecTxRpKXySFvpPlWUE6b3KwgOaoWt25nv4Lbk,1039
-mdkits/config/settings.yml,sha256=FY8lR5ffJrOen1O_Cnj28bsieQoG0DqagRRvgGc4s5I,71
-mdkits/mdkits.py,sha256=chj09AgBp1hMttyZgMj-OvQ0bH4zLCV4c-_pp4-sbmU,443
+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=SEJiJ8kqZIBBIE2pdOKwBSL8LqadWgA2_F0bk6e4xCg,443
 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
@@ -36,8 +36,8 @@ mdkits/util/fig_operation.py,sha256=FwffNUtXorMl6qE04FipgzcVljEQii7wrNJUCJMyY3E,
 mdkits/util/numpy_geo.py,sha256=ngSNoXkt3bHjOdv77ZlvQGbj1V75IyjjUWlDi1J0V6g,3549
 mdkits/util/os_operation.py,sha256=tNRjniDwFqARMy5Rf6MUNmaQGpJlyifCpuN16r8aB2g,828
 mdkits/util/structure_parsing.py,sha256=mRPMJeih3O-ST7HeETDvBEkfV-1psT-XgxyYgDadV0U,4152
-mdkits-0.1a2.dist-info/entry_points.txt,sha256=xoWWZ_yL87S501AzCO2ZjpnVuYkElC6z-8J3tmuIGXQ,44
-mdkits-0.1a2.dist-info/LICENSE,sha256=VLaqyB0r_H7y3hUntfpPWcE3OATTedHWI983htLftcQ,1081
-mdkits-0.1a2.dist-info/METADATA,sha256=dlhqxoOVcAMLz1yvFEytZY5jkHqHc8c7Kur3FIeW1EU,4284
-mdkits-0.1a2.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
-mdkits-0.1a2.dist-info/RECORD,,
+mdkits-0.1a4.dist-info/entry_points.txt,sha256=xoWWZ_yL87S501AzCO2ZjpnVuYkElC6z-8J3tmuIGXQ,44
+mdkits-0.1a4.dist-info/LICENSE,sha256=VLaqyB0r_H7y3hUntfpPWcE3OATTedHWI983htLftcQ,1081
+mdkits-0.1a4.dist-info/METADATA,sha256=5uPRWLj3rBwpqoKGxCgcaPT8sLDyUB1hkT_Nksueivg,4284
+mdkits-0.1a4.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
+mdkits-0.1a4.dist-info/RECORD,,