Merge branch 'v2.10'

plumed · Oct 10, 2024 · 49f558f · 49f558f · PlumedBot · Oct 10, 2024
2 parents 2dfbfc8 + 56789e9
commit 49f558f
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Showing 10 changed files with 70 additions and 3 deletions.
diff --git a/.github/workflows/linuxWF.yml b/.github/workflows/linuxWF.yml
@@ -28,6 +28,8 @@ jobs:
 # see https://github.com/plumed/plumed2/issues/976
         - -intel-
         - -pycv-mpi-
+#this does not install mpi but uses the internal one
+        - -nvhpc-mpi-
     steps:
     - uses: actions/checkout@v4
     - uses: actions/cache@v4
@@ -136,6 +138,18 @@ jobs:
         echo "CXX=icpx" >> $GITHUB_ENV
         echo "CC=icx" >> $GITHUB_ENV
         echo "FC=ifx" >> $GITHUB_ENV
+    - name: Install NVHPC compiler
+      if: contains( matrix.variant, '-nvhpc-' )
+      # use this if it does not work
+      # wget https://developer.download.nvidia.com/hpc-sdk/24.3/nvhpc_2024_243_Linux_x86_64_cuda_12.3.tar.gz
+      # tar xpzf nvhpc_2024_243_Linux_x86_64_cuda_12.3.tar.gz
+      # nvhpc_2024_243_Linux_x86_64_cuda_12.3/install
+      run: |
+        curl https://developer.download.nvidia.com/hpc-sdk/ubuntu/DEB-GPG-KEY-NVIDIA-HPC-SDK | sudo gpg --dearmor -o /usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg
+        echo 'deb [signed-by=/usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg] https://developer.download.nvidia.com/hpc-sdk/ubuntu/amd64 /' | sudo tee /etc/apt/sources.list.d/nvhpc.list
+        sudo apt-get update -y
+        sudo apt-get install -y nvhpc-24-3
+      # nvhpcinstalls his own mpi compilers
     - name: Install MPI
       # install MPI at last since it modifies CC and CXX
       if: contains( matrix.variant, '-mpi-' )

diff --git a/CHANGES/v2.9.md b/CHANGES/v2.9.md
@@ -63,3 +63,5 @@ Changes from version 2.8 which are relevant for users:
   - new patch for GROMACS 2024 
   - Small optimization of \ref COORDINATION and related collective variables (\issue{1096}).
 
+## Version 2.9.3 (tba)
+  - Patch for GROMACS 2024 was updated to fix a big issue preventing its use
diff --git a/developer-doc/.gitignore b/developer-doc/.gitignore
@@ -5,5 +5,6 @@
 /*PP.txt
 /links-to-user-manual.md
 /plumedcheck.md
-/coverage
+/coverage*/
+/coverage*
 
diff --git a/regtest/basic/rt-WALLS-sign/COLVAR.reference b/regtest/basic/rt-WALLS-sign/COLVAR.reference
@@ -0,0 +1,12 @@
+#! FIELDS time p.x uw1.bias lw1.bias uw2.bias lw2.bias uw3.bias lw3.bias uw4.bias lw4.bias uw1.force2 lw1.force2 uw2.force2 lw2.force2 uw3.force2 lw3.force2 uw4.force2 lw4.force2
+ 0.000000 -5.000000 0.000000 5.000000 0.000000 25.000000 0.000000 125.000000 0.000000 625.000000 0.000000 1.000000 0.000000 100.000000 0.000000 5625.000000 0.000000 250000.000000
+ 1.000000 -4.000000 0.000000 4.000000 0.000000 16.000000 0.000000 64.000000 0.000000 256.000000 0.000000 1.000000 0.000000 64.000000 0.000000 2304.000000 0.000000 65536.000000
+ 2.000000 -3.000000 0.000000 3.000000 0.000000 9.000000 0.000000 27.000000 0.000000 81.000000 0.000000 1.000000 0.000000 36.000000 0.000000 729.000000 0.000000 11664.000000
+ 3.000000 -2.000000 0.000000 2.000000 0.000000 4.000000 0.000000 8.000000 0.000000 16.000000 0.000000 1.000000 0.000000 16.000000 0.000000 144.000000 0.000000 1024.000000
+ 4.000000 -1.000000 0.000000 1.000000 0.000000 1.000000 0.000000 1.000000 0.000000 1.000000 0.000000 1.000000 0.000000 4.000000 0.000000 9.000000 0.000000 16.000000
+ 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
+ 6.000000 1.000000 1.000000 0.000000 1.000000 0.000000 1.000000 0.000000 1.000000 0.000000 1.000000 0.000000 4.000000 0.000000 9.000000 0.000000 16.000000 0.000000
+ 7.000000 2.000000 2.000000 0.000000 4.000000 0.000000 8.000000 0.000000 16.000000 0.000000 1.000000 0.000000 16.000000 0.000000 144.000000 0.000000 1024.000000 0.000000
+ 8.000000 3.000000 3.000000 0.000000 9.000000 0.000000 27.000000 0.000000 81.000000 0.000000 1.000000 0.000000 36.000000 0.000000 729.000000 0.000000 11664.000000 0.000000
+ 9.000000 4.000000 4.000000 0.000000 16.000000 0.000000 64.000000 0.000000 256.000000 0.000000 1.000000 0.000000 64.000000 0.000000 2304.000000 0.000000 65536.000000 0.000000
+ 10.000000 5.000000 5.000000 0.000000 25.000000 0.000000 125.000000 0.000000 625.000000 0.000000 1.000000 0.000000 100.000000 0.000000 5625.000000 0.000000 250000.000000 0.000000
diff --git a/regtest/basic/rt-WALLS-sign/Makefile b/regtest/basic/rt-WALLS-sign/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/basic/rt-WALLS-sign/config b/regtest/basic/rt-WALLS-sign/config
@@ -0,0 +1,11 @@
+type=driver
+arg="--plumed plumed.dat --ixyz trajectory.xyz"
+
+
+function plumed_regtest_before() {
+    for x in {-5..5}; do
+        echo "1" 
+        echo "100 100 100"
+        echo "C $x 0 0"
+    done > trajectory.xyz    
+}
diff --git a/regtest/basic/rt-WALLS-sign/der.reference b/regtest/basic/rt-WALLS-sign/der.reference
@@ -0,0 +1,12 @@
+#! FIELDS time parameter uw1.bias lw1.bias uw2.bias lw2.bias uw3.bias lw3.bias uw4.bias lw4.bias
+ 0.000000 0 0.000 -1.000 0.000 -10.000 0.000 -75.000 0.000 -500.000
+ 1.000000 0 0.000 -1.000 0.000 -8.000 0.000 -48.000 0.000 -256.000
+ 2.000000 0 0.000 -1.000 0.000 -6.000 0.000 -27.000 0.000 -108.000
+ 3.000000 0 0.000 -1.000 0.000 -4.000 0.000 -12.000 0.000 -32.000
+ 4.000000 0 0.000 -1.000 0.000 -2.000 0.000 -3.000 0.000 -4.000
+ 5.000000 0 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
+ 6.000000 0 1.000 0.000 2.000 0.000 3.000 0.000 4.000 0.000
+ 7.000000 0 1.000 0.000 4.000 0.000 12.000 0.000 32.000 0.000
+ 8.000000 0 1.000 0.000 6.000 0.000 27.000 0.000 108.000 0.000
+ 9.000000 0 1.000 0.000 8.000 0.000 48.000 0.000 256.000 0.000
+ 10.000000 0 1.000 0.000 10.000 0.000 75.000 0.000 500.000 0.000
diff --git a/regtest/basic/rt-WALLS-sign/plumed.dat b/regtest/basic/rt-WALLS-sign/plumed.dat
@@ -0,0 +1,13 @@
+p: POSITION ATOM=1 NOPBC
+
+uw1: UPPER_WALLS ARG=p.x AT=0 KAPPA=1.0 EXP=1
+lw1: LOWER_WALLS ARG=p.x AT=0 KAPPA=1.0 EXP=1
+uw2: UPPER_WALLS ARG=p.x AT=0 KAPPA=1.0 EXP=2
+lw2: LOWER_WALLS ARG=p.x AT=0 KAPPA=1.0 EXP=2
+uw3: UPPER_WALLS ARG=p.x AT=0 KAPPA=1.0 EXP=3
+lw3: LOWER_WALLS ARG=p.x AT=0 KAPPA=1.0 EXP=3
+uw4: UPPER_WALLS ARG=p.x AT=0 KAPPA=1.0 EXP=4
+lw4: LOWER_WALLS ARG=p.x AT=0 KAPPA=1.0 EXP=4
+
+PRINT ARG=p.x,*.bias,*.force2 FILE=COLVAR 
+DUMPDERIVATIVES ARG=*.bias FILE=der FMT=%04.3f
diff --git a/src/bias/Walls.cpp b/src/bias/Walls.cpp
@@ -94,7 +94,7 @@ Walls::Walls(const ActionOptions&ao):
       readInputLine( getShortcutLabel() + "_pow_" + argn + ": CUSTOM PERIODIC=NO FUNC=step(x)*x^" + exp[i] + " ARG=" + getShortcutLabel() + "_scale_" + argn );
     } else if( getName()=="LOWER_WALLS" ) {
       readInputLine( getShortcutLabel() + "_scale_" + argn + ": CUSTOM PERIODIC=NO FUNC=(x-" + offset[i] +")/" + eps[i] + " ARG=" + getShortcutLabel() + "_cv_" + argn );
-      readInputLine( getShortcutLabel() + "_pow_" + argn + ": CUSTOM PERIODIC=NO FUNC=step(-x)*x^" + exp[i] + " ARG=" + getShortcutLabel() + "_scale_" + argn );
+      readInputLine( getShortcutLabel() + "_pow_" + argn + ": CUSTOM PERIODIC=NO FUNC=step(-x)*(-x)^" + exp[i] + " ARG=" + getShortcutLabel() + "_scale_" + argn );
     }
     readInputLine( getShortcutLabel() + "_v_wall_" + argn + ": CUSTOM PERIODIC=NO FUNC=" + kappa[i] +"*x" + " ARG=" + getShortcutLabel() + "_pow_" + argn );
     readInputLine( getShortcutLabel() + "_wall_" + argn + ": SUM ARG=" + getShortcutLabel() + "_v_wall_" + argn + " PERIODIC=NO");

diff --git a/src/tools/MergeVectorTools.h b/src/tools/MergeVectorTools.h
@@ -51,7 +51,8 @@ static void mergeSortedVectors(const C* const* vecs, std::size_t size, std::vect
     /// to allow using a priority_queu, which selects the highest element.
     /// we here (counterintuitively) define < as >
     bool operator< (Entry const& rhs) const { return top() > rhs.top(); }
-    const auto & top() const { return *fwdIt; }
+    // TODO: revert "typename C::value_type" to "auto": nvc++ and icpc seems to do not deduce automatically the return type
+    const typename C::value_type & top() const { return *fwdIt; }
     void next() { ++fwdIt;};
   };