From ad5745ca5ba0a33ebc7538dee76436a1c6a90125 Mon Sep 17 00:00:00 2001 From: James Michael Goff Date: Wed, 13 Dec 2023 14:03:03 -0700 Subject: [PATCH] update install doc following lammps update --- README.md | 2 - docs/source/Installation.rst | 75 ++---------------------------------- 2 files changed, 3 insertions(+), 74 deletions(-) diff --git a/README.md b/README.md index 64043d064..435b4d44f 100644 --- a/README.md +++ b/README.md @@ -26,8 +26,6 @@ you're good to go! the Python package `mpi4py`. If installing mpi4py with a Python package manager, we recommend using pip over conda as pip will auto-configure your package to your system's defaut MPI version (usually what you used to build LAMMPS). -* [Optional] For atomic cluster expansion (ACE) capabilities, build LAMMPS with the ML-PACE package, -along with the `compute_pace` files from [https://github.com/jmgoff/lammps-user-pace](https://github.com/jmgoff/lammps-user-pace) #### Quick install (minimal working environment) using Conda: diff --git a/docs/source/Installation.rst b/docs/source/Installation.rst index 293acbc4d..0cf9dcfb2 100644 --- a/docs/source/Installation.rst +++ b/docs/source/Installation.rst @@ -18,8 +18,6 @@ Since LAMMPS is the backbone of FitSNAP, we begin with instructions on how to in specifically for using FitSNAP. The following few sections cover basics of installing LAMMPS with Python library support. -- If you want to fit ACE potentials, see `LAMMPS PACE install`_ - MPI for LAMMPS and FitSNAP ^^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -72,8 +70,6 @@ And see the output of running :code:`test.py` in parallel:: LAMMPS for FitSNAP ^^^^^^^^^^^^^^^^^^ -- If you want to fit ACE potentials, see `LAMMPS PACE install`_ - First clone the LAMMPS repo:: git clone https://github.com/lammps/lammps @@ -119,74 +115,9 @@ which should produce no errors. After completing this LAMMPS installation, please see `Install FitSNAP with latest LAMMPS`_ to use FitSNAP. -.. _LAMMPS PACE install: - -LAMMPS PACE install -^^^^^^^^^^^^^^^^^^^ - -Computes for ACE descriptors are currently in our modified LAMMPS repo (https://github.com/jmgoff/lammps_compute_PACE), -so the installation instructions are a little different if you want to use ACE. - -#. Clone our modified LAMMPS repo and set up a typical LAMMPS build:: - - git clone -b compute-pace https://github.com/jmgoff/lammps_compute_PACE - cd lammps_compute_PACE - mkdir build && cd build - -#. Set up a typical LAMMPS build the ML-PACE library enabled:: - - cmake ../cmake -DLAMMPS_EXCEPTIONS=yes \ - -DBUILD_SHARED_LIBS=yes \ - -DMLIAP_ENABLE_PYTHON=yes \ - -DPKG_PYTHON=yes \ - -DPKG_ML-SNAP=yes \ - -DPKG_ML-IAP=yes \ - -DPKG_ML-PACE=yes \ - -DPKG_SPIN=yes \ - -DPYTHON_EXECUTABLE:FILEPATH=`which python` - -#. Download the modified lammps-user-pace code that contains extra arrays for breaking out descriptor contributions:: - - git clone https://github.com/jmgoff/lammps-user-pace-1 - cp lammps-user-pace-1/ML-PACE/ace-evaluator/ace_evaluator.* ./lammps-user-pace-v.2022.10.15/ML-PACE/ace-evaluator/ - make -j - make install-python - - -#. Now, set up paths:: - - # Use DYLD_LIBRARY_PATH if using MacOS, on Linux use LD_LIBRARY_PATH: - export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/lammps_compute_PACE/build - -#. Now we can get and use FitSNAP:: - - cd /path/to/where/you/want/FitSNAP - git clone https://github.com/FitSNAP/FitSNAP - # Set python path so you can run FitSNAP as executable: - export PYTHONPATH=$PYTHONPATH:/path/to/where/you/want/FitSNAP - -Note for infrequent installation issues: For some versions of OMP, the -LAMMPS/PYTHON interface may produce errors when running, leading to a -LAMMPS exception that kills FitSNAP jobs. If your install completes -successfully and you have problems with the execution of examples in -the example folder, try recompiling lammps with these alternative -D flags. - -#. Alternative D flags for python/omp errors:: - - cmake ../cmake -D LAMMPS_EXCEPTIONS=on \ - -D PKG_PYTHON=on \ - -D BUILD_SHARED_LIBS=on \ - -D CMAKE_BUILD_TYPE=Debug \ - -D PKG_ML-IAP=on \ - -D PKG_ML-PACE=on \ - -D PKG_ML-SNAP=on \ - -D BUILD_MPI=on \ - -D BUILD_OMP=off \ - -D CMAKE_INSTALL_PREFIX=<$HOME>/.local \ - -D PKG_MOLECULE=on - -With key changes coming from turning off omp. +**NOTE:** There is no longer a need to use modified versions of LAMMPS or PACE libraries for ACE +model fitting. The :code:`compute pace` used by FitSNAP to calculate ACE descriptors is available +in the default branch of the public LAMMPS repository (https://github.com/lammps/lammps). For a summary/review of all these steps, see see `Quick Installation `__.