# FSATOOL-2.0

**Repository Path**: chen_changjun/fsatool-2.0

## Basic Information

- **Project Name**: FSATOOL-2.0
- **Description**: FSATOOL 2.0 is a molecular dynamics simulation and trajectory data analysis program. It is developped by Chen Changjun's group in Huazhong University of Science and Technology.
- **Primary Language**: FORTRAN
- **License**: AGPL-3.0
- **Default Branch**: master
- **Homepage**: https://gitee.com/chen_changjun/fsatool-2.0/wikis/pages
- **GVP Project**: No

## Statistics

- **Stars**: 4
- **Forks**: 0
- **Created**: 2021-06-22
- **Last Updated**: 2024-08-24

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# FSATOOL-2.0

#### 介绍 （Software Introduction）

FSATOOL 2.0 is a molecular dynamics simulation and trajectory data analysis program. It is developped by Chen Changjun's group in Huazhong University of Science and Technology.

#### 软件架构 (Software Architecture)

FSATOOL 2.0 constains many modules, including the simulation module (sim), Markov state model analysis module (msm) and trajectory data analysis
 module (analysis).

#### 软件下载 (Download)

# [FSATOOL on Github (latest version)](https://github.com/fsatool/fsatool.github.io)

# The source codes on Gitee are out of date.

#### 安装教程

How to install FSATOOL

1. Install NVIDIA HPC SDK (https://developer.nvidia.com/nvidia-hpc-sdk-downloads).
2. Compile NetCDF-Fortran and FFTW source codes by the nvfortran compiler.
   NetCDF (https://www.unidata.ucar.edu/software/netcdf/)
   FFTW (http://fftw.org/)
3. Set the environment variables NETCDFDIR and FFTWDIR with their directories.
4. Change to this directory and compile the source codes with the command "make".
5. Copy the generated executable file "fsatool" to any place you want to do the simulation or analysis work.

#### 使用说明

How to run FSATOOL

Execute the command "mpirun -n nproc fsatool modname taskname -i inputfile"

   "nproc" is the number of processes in the calculation.
   "modname" specifies the module to run.
   "taskname"(optional) gives the task name in each module.
   "inputfile"(optional) is a user-defined input parameter file. 

   All the available modname, taskname and default inputfiles are listed as follows:

   modname=sim,                           inputfile=sim.in
   modname=msm,                           inputfile=msm.in
                     taskname=cluster     inputfile=cluster.in
                     taskname=lumping     inputfile=lumping.in
                     taskname=tpt         inputfile=tpt.in
                     taskname=check       inputfile=check.in
                     taskname=tram        inputfile=tram.in
                     taskname=picksnap    inputfile=picksnap.in
   modname=analysis, taskname=wham,       inputfile=wham.in
                     taskanme=gmm,        inputfile=gmm.in
                     taskanme=freehis,    inputfile=freehis.in
                     taskanme=contactmap, inputfile=contactmap.in
                     taskanme=phi,        inputfile=phi.in
                     taskanme=anm,        inputfile=anm.in
                     taskanme=cv,         inputfile=cv.in
                     taskanme=reducedim,  inputfile=reducedim.in

Users can find more usages of FSATOOL in the supporting material of the following paper:

    Zirui Shu, Mincong Wu, Jun Liao and Changjun Chen*
    FSATOOL 2.0: An integrated molecular dynamics simulation and trajectory data analysis program.
    J. Comput. Chem. 2022, 43: 215-224.

or in the up-to-date reference manual on the web page:

    https://gitee.com/chen_changjun/fsatool-2.0/wikis/pages


#### 参与贡献

1.  Fork 本仓库
2.  新建 Feat_xxx 分支
3.  提交代码
4.  新建 Pull Request


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