USCCACS · TaufeqRazakh · Oct 3, 2025 · Oct 7, 2025 · Oct 8, 2025
diff --git a/README.md b/README.md
@@ -4,121 +4,153 @@
 
 ## 0. Prerequisites
 
-**rxmd** is designed to be simple, portable and minimally dependent on 3rd party library. You will need 1) a Fortran compiler that supports OpenMP, and 2) MPI (Message Passing Interface) library for parallel and distributed simulation. Modern Fortran compilers natively support OpenMP, and you can find many freely available MPI libraries online. Please refer to MPI library developer website about how to install their library. 
+**rxmd** is designed to be simple, portable and minimally dependent on 3rd party library. You will need 1) a Fortran compiler that supports OpenMP, and 2) MPI (Message Passing Interface) library for parallel and distributed simulation. Modern Fortran compilers natively support OpenMP, and you can find many freely available MPI libraries online. Please refer to MPI library developer website about how to install their library. 3) PyTorch machine learning framework 4) C++ Compiler
 
 **rxmd** has been tested on following environments.
 
-### - Fortan Compiler: 
+### Fortan Compiler: 
 ```
 GNU Fortran (GCC) 6.1.0
 Intel Fortran (IFORT) 17.0.4
 IBM XL Fortran V14.1
+Intel Fortran Compiler 2025.1
 ```
-### - MPI library: 
+
+### MPI library: 
 ```
 OpenMPI 1.8.8
 MPICH2
 MVAPICH2 
 Cray Mpich 7.6.0
+Intel MPI Library 2025.1
 ```
 
-## 1. Getting Started
+### PyTorch
+```
+PyTorch 2.8
+```
 
-To get started,  clone this repository to your computer. 
+### C++ Compiler
 ```
-~$ git clone https://github.com/USCCACS/rxmd.git
+Intel oneAPI DPC++/C++ Compiler 2025.1
+```
+
+## 1. Getting Started
+
+To get started, clone this repository to your computer. 
+```bash
+git clone https://github.com/USCCACS/rxmd.git
+cd rxmd
 ```
 
 ## 2. How to build RXMD
 
 ### 2.1 Working Directory
-Frist, change working directory to **rxmd/**
-```
-~$ cd rxmd-master
-```
-you will see following files and directories.
+After cloning, you will find the following directory structure in `rxmd`. `src/` contains all rxmd source codes and `init/` has a program and input files to generate an initial configurations for simulation. 
 
 ```
 rxmd $ ls
-DAT/          conf/         config/         ffield        regtests/     src/          util/
-make.inc      Makefile      doc/          init/         rxmd.in       unittests/
+.
+├── build.sh
+├── CMakeLists.txt
+├── config
+├── DAT
+├── docs
+├── examples
+├── init
+├── LICENSE.md
+├── pot
+├── README.md
+├── regtests
+├── rxmdtorch
+├── src
+├── unittests
+└── util
 ```
 
-Here, two directories, **src/** and **init/**, are especially important for you. **src/** contains all rxmd source codes and **init/** has a program and input files to generate an initial configurations for simulation. 
-
-### 2.2 Configure Makefiles
-
-There is an important file called **make.inc** that you might need to modify according to your computing environment. 
-
-- **make.inc** defines which compiler you like to use to build the **rxmd** and **geninit** executable. **geninit** is created inside **init/** directory and is used to generate intial configuration for simulation.
+### 2.2 Build with CMake
 
-- **config/** directory contains an example **make.inc** file called **make_example.inc**, and several other make.inc (make_hpc.inc,make_xl.inc) file containing predefined compiler settings for various machines. Copy the approprite file from **config/** inside the rxmd directory as make.inc. Each make.inc file has several compiler flags options. Enable the flags that you want use, and also do not forget disable macros you don't want to use. 
+Use the script `build.sh` uses CMake (min version 3.16) to manage building the source code on your hardware. This script will first build the `rxmdtorch` library and links it to create the `rxmd` executable in the `bin` directory.
 
-- **FC** variable in **make.inc**  is used to build software to generate intial configuration, called **geninit**. Any Fortran or MPI compiler that supports [the stream I/O](https://docs.oracle.com/cd/E19205-01/819-5262/aeuca/index.html) can be used here. 
+In order for CMake to find the necessary libraries and packages at the time of build generation, make sure of adding them to the PATH environment variable before using the build script.
 
-- **Makefile** contains commands to create the executable **geninit** and **rxmd**. For example, **make all** creates the executable **geninit** inside the the init folder and **rxmd** inside rxmd directory. Whereas, **make init** creates only the executable **geninit**  and  **make rxmd** creates **rxmd** executable.
+#### 2.2.1 Example build on Aurora
 
-- Each **init** and **src** has **Makefile** containing commands to create the executable **geninit** and **rxmd**, respectively. **Makefile** in rxmd directory calls these files to create the necessary executables.
+1. **Load a version of oneAPI and Python compiler**
+```bash
+module load cmake
+module load frameworks
+module use /soft/compilers/oneapi/2025.1.3/modulefiles/oneapi/public/
+module load 2025.1.3
+```
 
-Example 1) Linux Computer with Intel Compiler
+2. **Install IPEX and PyTorch version**
+The IPEX install must be suitable for the the oneAPI version which is loaded. Additionaly, it is recommended to do this in a Python virtual environment 
+```bash
+# Activate your virtual environment
+# source /path/to/new/venv/bin/activate
 
-Many HPC centers have Intel Fortran compiler and its MPI binding installed. If this is the case, copy the **make_hpc.inc** from **config/** as **make.inc**. It should look as shown below
+python -m pip install torch==2.8.0 torchvision==0.23.0 torchaudio==2.8.0 --index-url https://download.pytorch.org/whl/xpu
+python -m pip install intel-extension-for-pytorch==2.8.10+xpu oneccl_bind_pt==2.8.0+xpu --extra-index-url https://pytorch-extension.intel.com/release-whl/stable/xpu/us/
+```
+For newer versions of oneAPI/PyTorch, please refer the [IPEX page](https://github.com/intel/intel-extension-for-pytorch).
 
-- **make.inc** 
+3. **Build the project**
+You can either use CMake directly
+```bash
+cmake .. -DCMAKE_PREFIX_PATH=`python -c 'import torch; print(torch.utils.cmake_prefix_path)'`
+make -j 16
 ```
-# Intel Compiler
-MPIF90 = mpif90
-FC = ifort
+or run the provided build script.
+```bash
+sh build.sh
 ```
 
-### 2.3 Prepare Initial Geometry
+## 3. Preparing for a Simulation
 
-Next step is to generate initial MD geometry. Type the make command shown below. 
+### 3.1 Prepare Initial Geometry
 
-```
-rxmd $ make -C init/
-```
+Next step is to generate initial MD geometry. This is done with the `geninit.py` script in the `init/` directory.
 
-This compiles the standalone application **geninit**, read a geometry file (init.xyz by default) in **init/** directory, replicate the geometry and save the entire initial MD geometry into **rxff.bin** file, and then place **rxff.bin** file in **DAT/** directory. 
+`geninit.py` reads a geometry file (input.xyz by default), replicates it based on given parameters and saves the output geometry into `rxff.bin` file. The generated `rxff.bin` must be placed in the `DAT/` directory for the `rxmd` executable to find it.
 
-### 2.4 Build RXMD
+Example usage
+```bash
+cd init
+python geninit.py -i ../tobe.xyz -em ../rxmdnn.in
+cp rxff.bin ../DAT/
+cd ..
+```
 
-Type the command below to build the **rxmd** executable.
+### 3.2 Load Machine Learning Interatomic Potential Model
 
+The first line of the `rxmdnn.in` specfies the MLIP model and species parameters:
 ```
-rxmd $ make -C src/
+<model name> <path to MLIP model> <atomic number> [<species> <atomic number>]
 ```
 
-Check to see if you the **rxmd** executable and the initial geomerty input **DAT/rxff.bin** in place, then you are ready to start a simulation.
+A pre-trained model is available for downloaded [here](https://zenodo.org/records/14915165/files/afm256_01_HL.pt)
 
-```
-rxmd $ ls
-DAT/          conf/         ffield        regtests/     rxmd.in       unittests/
-Makefile.inc  doc/          init/         rxmd*         src/          util/
-```
-```
-rxmd $ ls DAT/
-rxff.bin
-```
+With the `rxmd` executable, initial geomerty input `DAT/rxff.bin` in place and the MLIP potential specified in `rxmdnn.in` with the species, you are ready to start a simulation.
 
-## 3. How to run
+## 4. How to run
 
-Default input parameters are set to run a single process job. In **rxmd.in**, the parameter **vprocs** defines how many MPI ranks in x, y, and z directions. Make sure you have **1 1 1** here. 
+By default, the input parameters are set to run as a single process. In `rxmd.in`, the parameter `vprocs` defines how many MPI ranks in x, y, and z directions. Make sure you have `1 1` here. 
 
 ```
-rxmd $ grep vprocs rxmd.in 
+$ grep vprocs rxmd.in 
 1 1 1                <vprocs>
 ```
 
-To run single MPI rank job on a typical Linux computer, you can simply type
-```
-rxmd $ ./rxmd
+To run a single MPI rank job from the project directory, execute
+```bash
+./bin/rxmd
 ```
 
-How to run a multi process job depends on which MPI library you use, but most likely **mpirun** just works for you. 
+To run a multi-process job, it depends on which MPI library you use, but most likely `mpirun` just works for you. 
 
-```
-rxmd $ mpirun -np nprocessors ./rxmd
+```bash
+mpirun -np nprocessors ./bin/rxmd
 ```
 
 If you see following outputs, congratulations! You have everything working.
@@ -169,12 +201,12 @@ nstep  TE  PE  KE: 1-Ebond 2-(Elnpr,Eover,Eunder) 3-(Eval,Epen,Ecoa) 4-(Etors,Ec
 
 To learn more about **rxmd**, please refer to [RXMD Manual](https://github.com/USCCACS/rxmd/blob/master/doc/ReaxFF/RXMDManual.md).
 
-## 4. License
+## 5. License
 
 This project is licensed under the GPL v3 license - see the [LICENSE.md](https://github.com/USCCACS/rxmd/blob/master/LICENSE.md) file for details
 
 
-## 5. Publications
+## 6. Publications
 * Mechanochemistry of shock-induced nanobubble collapse near silica in water
 K. Nomura, R. K. Kalia, A. Nakano, and P. Vashishta,
 [Applied Physics Letters 101, 073108: 1-4  (2012)](http://aip.scitation.org/doi/10.1063/1.4746270)

diff --git a/rxmdnn.in b/rxmdnn.in
@@ -1,2 +1,2 @@
 ## model path: element name, AMU
-allegro pot/ymno3.deploy 3  Y 88.90585 Mn 54.938044 O 15.9994
+allegro pot/afm256_01_HL.pt 89 H 1.008 He 4.002602 Li 6.94 Be 9.0121831 B 10.81 C 12.011 N 14.007 O 15.999 F 18.998403163 Ne 20.1797 Na 22.98976928 Mg 24.305 Al 26.9815385 Si 28.085 P 30.973761998 S 32.06 Cl 35.45 Ar 39.948 K 39.0983 Ca 40.078 Sc 44.955908 Ti 47.867 V 50.9415 Cr 51.9961 Mn 54.938044 Fe 55.845 Co 58.933194 Ni 58.6934 Cu 63.546 Zn 65.38 Ga 69.723 Ge 72.63 As 74.921595 Se 78.971 Br 79.904 Kr 83.798 Rb 85.4678 Sr 87.62 Y 88.90584 Zr 91.224 Nb 92.90637 Mo 95.95 Tc 97.90721 Ru 101.07 Rh 102.9055 Pd 106.42 Ag 107.8682 Cd 112.414 In 114.818 Sn 118.71 Sb 121.76 Te 127.6 I 126.90447 Xe 131.293 Cs 132.90545196 Ba 137.327 La 138.90547 Ce 140.116 Pr 140.90766 Nd 144.242 Pm 144.91276 Sm 150.36 Eu 151.964 Gd 157.25 Tb 158.92535 Dy 162.5 Ho 164.93033 Er 167.259 Tm 168.93422 Yb 173.054 Lu 174.9668 Hf 178.49 Ta 180.94788 W 183.84 Re 186.207 Os 190.23 Ir 192.217 Pt 195.084 Au 196.966569 Hg 200.592 Tl 204.38 Pb 207.2 Bi 208.9804 Ac 227.02775 Th 232.0377 Pa 231.03588 U 238.02891 Np 237.04817 Pu 244.06421
diff --git a/rxmdtorch/src/rxmdtorch.cpp b/rxmdtorch/src/rxmdtorch.cpp
@@ -26,7 +26,7 @@
 //#define BATCH_SIZE 1048576
 //
 
-#define AOTINDUCTOR
+//#define AOTINDUCTOR
 
 struct model_spec
 {