ACE grid computes with validation examples

build_note.sh

@@ -0,0 +1,50 @@
+#!/bin/bash
+
+mkdir build && cd build
+# Build and compile to use the fix python/gridforceace
+#NOTE first add your numpy include dir to your cplus include path
+export CPLUS_INCLUDE_PATH=$(python -c "import numpy; print(numpy.get_include())")
+
+cmake ../cmake -DLAMMPS_EXCEPTIONS=yes \
+               -DBUILD_SHARED_LIBS=yes \
+               -DBUILD_MPI=no \
+               -DBUILD_OMP=no \
+               -DPKG_PYTHON=yes \
+               -DPKG_ML-SNAP=yes \
+               -DPKG_ML-PACE=yes \
+               -DPKG_ML-IAP=yes \
+               -DPKG_MLIAP_ENABLE_PYTHON=yes \
+               -DPYTHON_EXECUTABLE:FILEPATH=`which python` \
+               -DPYTHON_INCLUDE_DIR=$(python -c "import sysconfig; print(sysconfig.get_path('include'))")  \
+               -DPYTHON_LIBRARY=$(python -c "import sysconfig; print(sysconfig.get_config_var('LIBDIR'))") 
+
+make -j
+make install-python
+
+# To compile and build when only using the ace grid computes
+
+cmake ../cmake -DLAMMPS_EXCEPTIONS=yes \
+               -DBUILD_SHARED_LIBS=yes \
+               -DBUILD_MPI=yes \
+               -DBUILD_OMP=yes \
+               -DPKG_PYTHON=yes \
+               -DPKG_ML-SNAP=yes \
+               -DPKG_ML-PACE=yes \
+               -DPKG_ML-IAP=yes \
+               -DPKG_MLIAP_ENABLE_PYTHON=yes \
+               -DPYTHON_EXECUTABLE:FILEPATH=`which python` \
+               -DPYTHON_INCLUDE_DIR=$(python -c "import sysconfig; print(sysconfig.get_path('include'))")  \
+               -DPYTHON_LIBRARY=$(python -c "import sysconfig; print(sysconfig.get_config_var('LIBDIR'))") 
+
+make -j
+make install-python
+
+#NOTE that the following dflags were optional in both cases above:
+#               -DPKG_ML-IAP=yes \
+#               -DPKG_MLIAP_ENABLE_PYTHON=yes \
+
+#tested with:
+#cmake version 3.26.5
+#Python 3.10.13
+#Numpy 1.26.4
+#gcc (GCC) 8.5.0

cmake/Modules/Packages/ML-PACE.cmake

@@ -1,33 +1,40 @@
-set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.01.3.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
 
-set(PACELIB_MD5 "4f0b3b5b14456fe9a73b447de3765caa" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+set(PACELIB_MD5 "b45de9a633f42ed65422567e3ce56f9f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
 mark_as_advanced(PACELIB_URL)
 mark_as_advanced(PACELIB_MD5)
 GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)
 
-# download library sources to build folder
-if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
-  file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
-endif()
-if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
-  message(STATUS "Downloading ${PACELIB_URL}")
-  file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
-  file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
-  if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}"))
-    message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
-    file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
-  endif()
+# LOCAL_ML-PACE points to top-level dir with local lammps-user-pace repo,
+# to make it easier to check local build without going through the public github releases
+if(LOCAL_ML-PACE)
+ set(lib-pace "${LOCAL_ML-PACE}")
 else()
-  message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
-endif()
+  # download library sources to build folder
+  if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
+    file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
+  endif()
+  if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
+    message(STATUS "Downloading ${PACELIB_URL}")
+    file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
+    file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
+    if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}"))
+      message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
+      file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
+    endif()
+  else()
+    message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
+  endif()
+
 
-# uncompress downloaded sources
-execute_process(
-  COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
-  COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
-  WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-)
-get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
+  # uncompress downloaded sources
+  execute_process(
+    COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
+    COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
+    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+  )
+  get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
+endif()
 
 add_subdirectory(${lib-pace} build-pace)
 set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})

examples/python/betas_python.py

@@ -0,0 +1,71 @@
+from __future__ import print_function
+from lammps import lammps
+import ctypes
+import numpy as np
+from ctypes import *
+
+#NOTE you may import mala functions here
+#import mala.  
+
+flat_beta = True
+def get_grid(ngrid):
+    igrid = 0
+    for nx in range(ngrid):
+        for ny in range(ngrid):
+            for nz in range(ngrid):
+                igrid += 1
+    return igrid
+
+from numpy.random import RandomState
+def pre_force_callback(lmp):
+    L = lammps(ptr=lmp)
+
+    def _extract_compute_np(lmp, name, compute_style, result_type, array_shape=None):
+        if array_shape is None:
+            array_np = lmp.numpy.extract_compute(name,compute_style, result_type)
+        else:
+            ptr = lmp.extract_compute(name, compute_style, result_type)
+            if result_type == 0:
+
+                # no casting needed, lammps.py already works
+
+                return ptr
+            if result_type == 2:
+                ptr = ptr.contents
+            total_size = np.prod(array_shape)
+            buffer_ptr = ctypes.cast(ptr, ctypes.POINTER(ctypes.c_double * total_size))
+            array_np = np.frombuffer(buffer_ptr.contents, dtype=float)
+            array_np.shape = array_shape
+        return array_np
+
+    #-------------------------------------------------------------
+    # variables to access fix pointer in python if needed
+    #-------------------------------------------------------------
+    #fid = 'python/gridforceace' # id for the fix
+    fid = '4'
+    ftype = 2 # 0 for scalar 1 for vector 2 for array
+    result_type = 2
+    compute_style = 0
+    fstyle = 0
+
+    ncolbase = 0
+    nrow = (get_grid(ngrid=3)) #for now add a dE_I/dB_{I,K}row for ALL gridpoints (global)
+    ncoef = int(368/2) #number of ace descriptors per atom - may be obtained from ACE functions in mala
+    ncol = ncoef + ncolbase
+    # set to 1 if including energy row
+    #base_array_rows = 1
+    base_array_rows=0
+    #-------------------------------------------------------------
+    # dummy function to get dE_I/dB_{I,k} for a
+    #-------------------------------------------------------------
+    prng = RandomState(3481)
+    betas_row = prng.uniform(-1,1,ncoef)*1.e-2 #np.arange(ncoef)*1.e-6
+    betas = np.repeat(np.array([betas_row]),repeats = nrow+base_array_rows,axis=0)
+
+    #-------------------------------------------------------------
+    if flat_beta:
+        betas = betas.flatten()
+        return np.ascontiguousarray(betas)
+    else:
+        return betas
+