This has been developed with the central purpose of developing semi-empirical models from quantum simulations and x-ray diffraction data. They should be generally useful for anyone running VASP or LAMMPS simulations, as well those studying x-ray diffraction patterns. Use it as you please, feel free to modify, chop-up or ruin this code as much as you like. Programs will tell you how to run them if run without any arguements, in general the name of the code should be self explanatory. Feel free to contact me with requests.
Required Libraries
==================
* python-numpy (generic math and numerics toolkit)
* python-scipy (generic science toolkit)
* python-matplotlib (2-D plotting)
* python-mayavi2 (3-d plotting)
* qhull & qvoronoi (voronoi and neighbor analysis)
Optional Libraries
==================
* python-gtk2
* LAMMPS compiled with a python wrapper, with lammps.py in the PYTHONPATH
Description
-----------
* **analysis** - Generic tools for manipulating data and generating analyses with many applications e.g.: FFTs, band pass, multidimensional curve fitting, etc.
* **diffraction** - Tools for x-ray pattern analysis and some curve fitting.
* **gmice** - A couple of tools for running codes remotely on our HPC server.
* **moldyn** - Scripts for reading LAMMPS molecular dynamics output data, some analysis and plotting.
* **vasp** - Scripts that plot and post-process VASP output data.
* **potfitting** - Tools for potential fitting and analyzing potentials.
* **plotremote** - tools for running these scripts from a remote server, makes working remotely easier when coupled with a file transfer system like dropbox.
To Install
----------
Edit your .bashrc (or equivalent) and add:
```bash
matcalcdir="/path/to/matcalc/repo"
matcalcsubdirs=${matcalcdir}:$(find ${matcalcdir} -maxdepth 1 -type d | tr '\n' ':' | sed 's/:$//')
export PYTHONPATH=$PYTHONPATH:${matcalcsubdirs}
export PATH=$PATH:${matcalcsubdirs}
```
Examples
--------
* Plot your POSCAR with a handy 3-D visualizer:
```bash
poscarPlot.py POSCAR
```
* Plot the energy vs time of your OUTCAR:
```bash
outcarPlotETime.py OUTCAR
```
* Generate a gorgeous equation of state plot from a collection of OUTCARs, can even compare against an empirical potential
```bash
outcarsPlotEOS.py dir/to/eos/files Cu_lammps.eam
```
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matcalc:用于生成和分析模拟的脚本集合,用于计算材料科学
共194个文件
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2021-05-31
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其开发的核心目的是根据量子模拟和 X 射线衍射数据开发半经验模型。 它们通常对运行 VASP 或 LAMMPS 模拟的任何人以及研究 X 射线衍射图案的人有用。 随意使用它,随意修改、删除或破坏此代码。 程序会告诉你如何在没有任何争论的情况下运行它们,通常代码的名称应该是不言自明的。 如有要求,请随时与我联系。 所需的图书馆 python-numpy(通用数学和数字工具包) python-scipy(通用科学工具包) python-matplotlib(二维绘图) python-mayavi2(3维绘图) qhull & qvoronoi(voronoi 和邻居分析) 可选库 Python-gtk2 用 python 包装器编译的 LAMMPS,在 PYTHONPATH 中使用 lammps.py 描述 分析- 用于处理数据和生成具有许多应用程序的分析的通用工具,例如:FFT、带
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matcalc:用于生成和分析模拟的脚本集合,用于计算材料科学 (194个子文件)
dump.dat 1.2MB
.gitignore 16B
rdftest.go 5KB
blah.go 1KB
mtrlTypes.go 145B
gotest 1.44MB
INCAR_dos 503B
INCAR_precise 976B
KPOINTS_dos 46B
README.md 2KB
points.png 36KB
poscarRDF.png 28KB
POSCAR 16KB
POSCAR2 9KB
POSCAR_large 2.79MB
charter.py 15KB
plot2.py 14KB
fieldPointAnalysis.py 13KB
rdf.py 13KB
orderParam.py 13KB
plot3.py 12KB
grabcluster.py 12KB
lammpsIO.py 12KB
ISFCriteria.py 11KB
sf.py 11KB
ISFRMSD.py 10KB
rootMeanSquareDist.py 9KB
grabclusterxdat.py 9KB
vanHove.py 9KB
potfitPrepADP2.py 9KB
outcarIO.py 8KB
outcarsPlotEOS.py 8KB
neighbors.py 8KB
elfcarVisualize.py 8KB
struct_tools.py 8KB
ISF.py 8KB
poscarChart.py 7KB
ISFTetra.py 6KB
potfitPrepADP.py 6KB
plotADP.py 6KB
elfcarBond.py 6KB
potfitPurgeFDB.py 6KB
rdfExtend.py 5KB
scan_oc.py 5KB
doscarSmoothPlot.py 5KB
ensembleISFS.py 5KB
vizlmpdmp.py 5KB
procarIO.py 5KB
geometry.py 5KB
elfcarCoordination.py 5KB
chgcarLengthAnalysis.py 5KB
rmsdAnalysis.py 5KB
chgcarBondPlaneAverage.py 4KB
xdatcarPathsFading.py 4KB
xdatcarPath.py 4KB
plotuspexbest.py 4KB
RDFCriteria.py 4KB
chgcarVacancy.py 4KB
xdatcarPathOrderParam.py 4KB
outcar2Coordination.py 4KB
chgcarBondVolumeAverage.py 4KB
interpolate.py 4KB
bondSoftnessRender.py 4KB
poscarIO.py 4KB
outcar2atomInfo.py 4KB
poscarBaxter.py 4KB
outcar2columns.py 4KB
chgcarIsosurf.py 4KB
hopAnalysis.py 3KB
doscarPlot.py 3KB
outcarPlotMSDAtom.py 3KB
potfitScaleFDB.py 3KB
dumpPlot.py 3KB
dumpPlotDiff.py 3KB
compareAdpVaspFeedback.py 3KB
gaussFunctions.py 3KB
datatools.py 3KB
genlattice_lammps.py 3KB
lammps_genlattice.py 3KB
geniniteampot.py 3KB
elfcarBondAnalyze.py 3KB
procarPlot.py 3KB
potfitFDB2poscar.py 3KB
potfitOutcar2FDB.py 3KB
chgcarIO.py 3KB
doscarsPlot.py 3KB
outcarPathways.py 3KB
poscar2Coordination.py 3KB
poscarGrow.py 3KB
plotstruct.py 3KB
ensembleNeighbors.py 2KB
parserGens.py 2KB
potfitStressErrHist.py 2KB
potfitEnergyErrHist.py 2KB
ensembleBondOrder.py 2KB
ensembleCoord.py 2KB
ensembleTetra.py 2KB
elfcar2bodyCorrelation.py 2KB
potfitPlotSampleADP.py 2KB
genlattice.py 2KB
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