Multiple updates to metatomic integration

.ci/pytorch/requirements.txt

@@ -1,5 +1,5 @@
 # The extra url makes pip grap the torch fersion we want to use in the regtests
 --extra-index-url=https://download.pytorch.org/whl/cpu
 torch>=2.7
-metatomic-torch>=0.1.3,<0.2
-featomic-torch==0.7.0
+metatomic-torch>=0.1.8,<0.2
+featomic-torch>=0.7.0,<0.8

.github/workflows/linuxWF.yml

@@ -87,7 +87,21 @@ jobs:
               MDAnalysis
         pip install --user -r ./.ci/pytorch/requirements.txt
 
-        # torch 2.7 above is the first one to use cxx11 ABI for the PyPI wheels
+        python -c "import featomic.torch; print('featomic.torch.__file__:', featomic.torch.__file__)"
+
+        echo "ls /home/runner/.local/lib/python3.10/site-packages/featomic/torch/"
+        ls /home/runner/.local/lib/python3.10/site-packages/featomic/torch/
+
+        echo "ls /home/runner/.local/lib/python3.10/site-packages/featomic_torch.libs/"
+        ls /home/runner/.local/lib/python3.10/site-packages/featomic_torch.libs/
+
+        python -c "import featomic.torch; import metatomic.torch; print(metatomic.torch._extensions._collect_extensions('/tmp/ext-test'))"
+
+        python -c "import site; print('getsitepackages:', site.getsitepackages())"
+        python -c "import site; print('getusersitepackages:', site.getusersitepackages())"
+
+        exit 1
+
 
     - name: Configure libmetatomic & libtorch
       if: ${{ ! contains( matrix.variant, '-debug-' ) }} # the libraries on PyPI are not compiled with GLIBCXX_DEBUG

configure

@@ -10007,8 +10007,8 @@ $as_echo_n "checking libmetatomic without extra libs... " >&6; }
     #include <metatensor.hpp>
     #include <metatensor/torch.hpp>
     #include <metatomic/torch.hpp>
-    #if METATOMIC_TORCH_VERSION_MAJOR != 0 || METATOMIC_TORCH_VERSION_MINOR != 1
-    #error "this code is only compatible with metatomic-torch >=0.1,<0.2"
+    #if METATOMIC_TORCH_VERSION_MAJOR != 0 || METATOMIC_TORCH_VERSION_MINOR != 1 || METATOMIC_TORCH_VERSION_PATCH < 8
+    #error "this code is only compatible with metatomic-torch >=0.1.8,<0.2"
     #endif
     int main() {
       metatomic_torch::version();
@@ -10056,8 +10056,8 @@ $as_echo_n "checking libmetatomic with $all_LIBS... " >&6; }
     #include <metatensor.hpp>
     #include <metatensor/torch.hpp>
     #include <metatomic/torch.hpp>
-    #if METATOMIC_TORCH_VERSION_MAJOR != 0 || METATOMIC_TORCH_VERSION_MINOR != 1
-    #error "this code is only compatible with metatomic-torch >=0.1,<0.2"
+    #if METATOMIC_TORCH_VERSION_MAJOR != 0 || METATOMIC_TORCH_VERSION_MINOR != 1 || METATOMIC_TORCH_VERSION_PATCH < 8
+    #error "this code is only compatible with metatomic-torch >=0.1.8,<0.2"
     #endif
     int main() {
       metatomic_torch::version();
@@ -10105,8 +10105,8 @@ $as_echo_n "checking libmetatomic with -l$testlib... " >&6; }
     #include <metatensor.hpp>
     #include <metatensor/torch.hpp>
     #include <metatomic/torch.hpp>
-    #if METATOMIC_TORCH_VERSION_MAJOR != 0 || METATOMIC_TORCH_VERSION_MINOR != 1
-    #error "this code is only compatible with metatomic-torch >=0.1,<0.2"
+    #if METATOMIC_TORCH_VERSION_MAJOR != 0 || METATOMIC_TORCH_VERSION_MINOR != 1 || METATOMIC_TORCH_VERSION_PATCH < 8
+    #error "this code is only compatible with metatomic-torch >=0.1.8,<0.2"
     #endif
     int main() {
       metatomic_torch::version();

configure.ac

@@ -989,8 +989,8 @@ if test $libmetatomic = true ; then
     #include <metatensor.hpp>
     #include <metatensor/torch.hpp>
     #include <metatomic/torch.hpp>
-    #if METATOMIC_TORCH_VERSION_MAJOR != 0 || METATOMIC_TORCH_VERSION_MINOR != 1
-    #error "this code is only compatible with metatomic-torch >=0.1,<0.2"
+    #if METATOMIC_TORCH_VERSION_MAJOR != 0 || METATOMIC_TORCH_VERSION_MINOR != 1 || METATOMIC_TORCH_VERSION_PATCH < 8
+    #error "this code is only compatible with metatomic-torch >=0.1.8,<0.2"
     #endif
     int main() {
       metatomic_torch::version();

regtest/metatomic/rt-basic/cv.py

@@ -32,28 +32,29 @@ class TestCollectiveVariable(torch.nn.Module):
     CV^2 are returned.
     """
 
-    def __init__(self, cutoff, multiple_properties):
+    def __init__(self, cutoff, multiple_properties, features_key="features"):
         super().__init__()
 
         self._nl_request = NeighborListOptions(
             cutoff=cutoff, full_list=True, strict=True
         )
         self._multiple_properties = multiple_properties
+        self._features_key = features_key
 
     def forward(
         self,
         systems: List[System],
         outputs: Dict[str, ModelOutput],
         selected_atoms: Optional[Labels],
     ) -> Dict[str, TensorMap]:
-        if "features" not in outputs:
+        if self._features_key not in outputs:
             return {}
 
         device = torch.device("cpu")
         if len(systems) > 0:
             device = systems[0].positions.device
 
-        output = outputs["features"]
+        output = outputs[self._features_key]
 
         if output.per_atom:
             samples_list: List[List[int]] = []
@@ -123,7 +124,7 @@ def forward(
                     "selected atoms is only supported with per-atom output"
                 )
 
-        return {"features": cv}
+        return {self._features_key: cv}
 
     def requested_neighbor_lists(self) -> List[NeighborListOptions]:
         return [self._nl_request]
@@ -169,3 +170,12 @@ def requested_neighbor_lists(self) -> List[NeighborListOptions]:
 cv.eval()
 model = AtomisticModel(cv, ModelMetadata(), capabilities)
 model.save("vector-global.pt")
+
+
+cv = TestCollectiveVariable(
+    cutoff=CUTOFF, multiple_properties=False, features_key="features/variant"
+)
+capabilities.outputs = {"features/variant": ModelOutput(per_atom=False)}
+cv.eval()
+model = AtomisticModel(cv, ModelMetadata(), capabilities)
+model.save("variant-global.pt")

regtest/metatomic/rt-basic/forces.reference

@@ -1,11 +1,11 @@
 9
--4795.88 -5679.30 -5054.72
-X   147.18   -79.30  -178.34
-X  -174.21   -55.39   124.40
-X  -214.90    78.13   151.48
-X  -424.19   203.64   276.74
-X    71.31   -44.07    35.23
-X   230.71  -150.74  -438.92
-X   140.70   -55.57   -67.27
-X   208.55   -18.70   211.20
-X    14.85   122.00  -114.51
+-4822.75 -5711.13 -5083.06
+X   148.00   -79.74  -179.33
+X  -175.19   -55.70   125.09
+X  -216.11    78.57   152.33
+X  -426.55   204.77   278.27
+X    71.71   -44.32    35.43
+X   231.98  -151.58  -441.35
+X   141.49   -55.88   -67.65
+X   209.72   -18.80   212.37
+X    14.94   122.68  -115.16

regtest/metatomic/rt-basic/plumed.dat

@@ -55,15 +55,28 @@ vector_per_atom: METATOMIC ...
 
 PRINT ARG=vector_per_atom FILE=vector_per_atom FMT=%8.2f
 
+variant: METATOMIC ...
+      MODEL=variant-global.pt
+      VARIANT=variant
+      DEVICE=cpu
+
+      SPECIES1=1,4,7
+      SPECIES2=2,3,5,6,8,9
+      SPECIES_TO_TYPES=6,8
+...
+
+PRINT ARG=variant FILE=variant FMT=%8.2f
+
 
 scalar_per_atom_sum: SUM ARG=scalar_per_atom PERIODIC=NO
 vector_global_sum: SUM ARG=vector_global PERIODIC=NO
 vector_per_atom_sum: SUM ARG=vector_per_atom PERIODIC=NO
+variant_sum: SUM ARG=variant PERIODIC=NO
 
 summed: CUSTOM ...
-      ARG=scalar_global,scalar_per_atom_sum,vector_global_sum,vector_per_atom_sum
-      VAR=x,y,z,t
-      FUNC=x+y+z+t
+      ARG=scalar_global,scalar_per_atom_sum,vector_global_sum,vector_per_atom_sum,variant_sum
+      VAR=a,b,c,d,e
+      FUNC=a+b+c+d+e
       PERIODIC=NO
 ...
 

src/maketools/codecheck

@@ -75,6 +75,7 @@ fi
       -U__PLUMED_HAS_ASMJIT \
       -D__PLUMED_WRAPPER_CXX_EXPLICIT=explicit \
       --config-exclude=small_vector/ \
+      -i vesin.cpp \
       --template='[{file}:{line}] ({severity}) :{id}: {message}' \
       --enable=all --suppress=missingIncludeSystem --inline-suppr --force \
       $files

src/metatomic/import.sh → src/metatomic/import-vesin.sh

@@ -1,21 +1,19 @@
 #!/usr/bin/env bash
 
-path=$1
+version=$1
 
 if (($# != 1)) ; then
-echo "usage: $0 /path/to/vesin"
-echo
-echo "All the commands to run:"
-echo "    cd /some/dir/"
-echo "    git clone https://github.com/luthaf/vesin"
-echo "    cd /your/plumed2/src/metatomic"
-echo "    ./import.sh /some/dir/vesin"
-exit 0
+echo "usage: $0 <vesin-version>"
+exit 1
 fi
 
-bash -c "$path/create-single-cpp.py > /dev/null"
+rm -f vesin-single-build-v*.tar.gz
+wget https://github.com/Luthaf/vesin/releases/download/v$version/vesin-single-build-v$version.tar.gz
 
-cp $path/vesin/include/vesin.h vesin.h
+tar xf vesin-single-build-v$version.tar.gz
+# bash -c "$path/create-single-cpp.py > /dev/null"
+
+# cp $path/vesin/include/vesin.h vesin.h
 mv vesin-single-build.cpp vesin.cpp
 
 # Patch files to follow PLUMED linter
@@ -28,7 +26,7 @@ sed 's|#define VESIN_H|#define VESIN_H\n/*INDENT-OFF*/\n|
     ' vesin.h > tmp
 mv tmp vesin.h
 
-sed '1 s|^|/*INDENT-OFF*/\n#include "vesin.h"\n|
+sed '1 s|^|/*INDENT-OFF*/\n|
      s|<stddef.h>|<cstddef>|
      s|<stdint.h>|<cstdint>|
      s|vesin::|PLMD::metatomic::vesin::|