Merge branch 'master' into fix-newmac-arm-issues

.github/workflows/linuxWF.yml

@@ -26,7 +26,7 @@ jobs:
         - -debug-mpi-
 # temporarily commented out
 # see https://github.com/plumed/plumed2/issues/976
-#        - -intel-
+        - -intel-
     steps:
     - uses: actions/checkout@v4
     - uses: actions/cache@v3
@@ -113,17 +113,21 @@ jobs:
       # install INTEL at last since it modifies CC and CXX
       if: contains( matrix.variant, '-intel-' )
       run: |
-        wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
-        sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
-        rm GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
+        wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+        sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+        rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+        #wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
+        #sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
+        #rm GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
         echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
         sudo apt-get update
-        sudo apt-get install intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic intel-oneapi-mkl intel-oneapi-mkl-devel intel-oneapi-compiler-fortran
+        #sudo apt-get install intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic intel-oneapi-mkl intel-oneapi-mkl-devel intel-oneapi-compiler-fortran
+        sudo apt-get install intel-basekit intel-hpckit 
         source /opt/intel/oneapi/setvars.sh
         printenv >> $GITHUB_ENV
-        echo "CXX=icpc" >> $GITHUB_ENV
-        echo "CC=icc" >> $GITHUB_ENV
-        echo "FC=ifort" >> $GITHUB_ENV
+        echo "CXX=icpx" >> $GITHUB_ENV
+        echo "CC=icx" >> $GITHUB_ENV
+        echo "FC=ifx" >> $GITHUB_ENV
     - name: Install MPI
       # install MPI at last since it modifies CC and CXX
       if: contains( matrix.variant, '-mpi-' )

regtest/basic/rt-NeigbourlistInitialization/Makefile

@@ -0,0 +1 @@
+include ../../scripts/test.make

regtest/basic/rt-NeigbourlistInitialization/config

@@ -0,0 +1 @@
+type=make

regtest/basic/rt-NeigbourlistInitialization/main.cpp

@@ -0,0 +1,132 @@
+#include "plumed/tools/AtomNumber.h"
+#include "plumed/tools/Communicator.h"
+#include "plumed/tools/NeighborList.h"
+#include "plumed/tools/Pbc.h"
+#include <fstream>
+#include <iostream>
+
+using PLMD::AtomNumber;
+using PLMD::Communicator;
+using PLMD::NeighborList;
+using PLMD::Pbc;
+
+// Testing that the Neigbour list will be intialized with the desired number of
+// couples
+// We are initializing with distance and stride not set to check the default
+// parameters
+
+#define check(arg) (((arg)) ? "pass\n" : "not pass\n")
+
+int main(int, char **) {
+  std::ofstream report("unitTest");
+  Pbc pbc{};
+  pbc.setBox(PLMD::Tensor({1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0}));
+  Communicator cm{};
+  bool serial = true;
+  bool do_pbc = false;
+  for (const size_t nat0 : {100, 500, 1000, 10000}) {
+    std::vector<AtomNumber> list0(nat0);
+    size_t i = 0;
+    for (auto &an : list0) {
+      an.setIndex(i);
+      ++i;
+    }
+    {
+      report << "Single list:\n";
+      std::string prepend="["+std::to_string(nat0)+"]";
+      size_t expected = ((nat0 - 1) * nat0) / 2;
+      auto nl = NeighborList(list0, serial, do_pbc, pbc, cm);
+
+      bool expectedcouples = true;
+      {
+        size_t cID = 0;
+        for (size_t i0 = 0; i0 < nat0 && expectedcouples; ++i0) {
+          for (size_t i1 = i0+1; i1 < nat0 && expectedcouples; ++i1) {  
+            auto couple = nl.getClosePair(cID);
+            expectedcouples &= couple.first == i0;
+            expectedcouples &= couple.second == i1;
+            ++cID;
+          }
+        }
+      }
+      report << prepend << "Initial number:      "
+        << check(nl.size() == expected);
+      report << prepend << "getIndexPair():      "
+        << check(expectedcouples);
+      report << prepend << "Lastupdate is 0:     "
+        << check(nl.getLastUpdate() == 0);
+      report << prepend << "Default stride is 0: "
+          << check(nl.getStride() == 0);
+      report << "\n";
+    }
+    for (const size_t nat1 : {100, 500, 1000, 10000}) {
+
+      std::vector<AtomNumber> list1(nat1);
+
+      i = 0;
+      for (auto &an : list1) {
+        an.setIndex(i);
+        ++i;
+      }
+
+      {
+        report << "Double list, no pairs:\n";
+        std::string prepend="["+std::to_string(nat0)
+            + ", " + std::to_string(nat1)  +"]";
+        bool do_pair = false;
+        size_t expected = nat1 * nat0;
+        auto nl = NeighborList(list0, list1, serial, do_pair, do_pbc, pbc, cm);
+
+        bool expectedcouples = true;
+        {
+          size_t cID = 0;
+          for (size_t i0 = 0; i0 < nat0 && expectedcouples; ++i0) {
+            for (size_t i1 = 0; i1 < nat1 && expectedcouples; ++i1) {
+              auto couple = nl.getClosePair(cID);
+              //The getIndexPair for non couple input must return this be this
+              //(cID / nat1);
+              expectedcouples &= couple.first == i0;
+              //(cID % nat1 + nat0);
+              expectedcouples &= couple.second == nat0+i1;
+              ++cID;
+            }
+          }
+        }
+        report << prepend << "Initial number:      "
+          << check(nl.size() == expected);
+        report << prepend << "getIndexPair():      "
+          << check(expectedcouples);
+        report << prepend << "Lastupdate is 0:     "
+          << check(nl.getLastUpdate() == 0);
+        report << prepend << "Default stride is 0: "
+          << check(nl.getStride() == 0);
+        report << "\n";
+      }
+
+      if (nat1 == nat0) {
+        report << "Double list, with pairs:\n";
+        std::string prepend="["+std::to_string(nat0)
+            + ", " + std::to_string(nat1) +"]";
+        bool do_pair = true;
+        size_t expected = nat0;
+        auto nl = NeighborList(list0, list1, serial, do_pair, do_pbc, pbc, cm);
+
+        bool expectedcouples = true;
+        for (size_t cID = 0; cID < nat0 && expectedcouples; ++cID) {
+          auto couple = nl.getClosePair(cID);
+          expectedcouples &= couple.first == cID;
+          expectedcouples &= couple.second == cID + nat0;
+        }
+        report << prepend << "Initial number:      " 
+          << check(nl.size() == expected);
+        report << prepend << "getIndexPair():      "
+          << check(expectedcouples);
+        report << prepend <<  "Lastupdate is 0:     " 
+          << check(nl.getLastUpdate() == 0);
+        report << prepend << "Default stride is 0: "
+          << check(nl.getStride() == 0);
+        report << "\n";
+      }
+    }
+  }
+}

regtest/basic/rt-NeigbourlistInitialization/unitTest.reference

@@ -0,0 +1,144 @@
+Single list:
+[100]Initial number:      pass
+[100]getIndexPair():      pass
+[100]Lastupdate is 0:     pass
+[100]Default stride is 0: pass
+
+Double list, no pairs:
+[100, 100]Initial number:      pass
+[100, 100]getIndexPair():      pass
+[100, 100]Lastupdate is 0:     pass
+[100, 100]Default stride is 0: pass
+
+Double list, with pairs:
+[100, 100]Initial number:      pass
+[100, 100]getIndexPair():      pass
+[100, 100]Lastupdate is 0:     pass
+[100, 100]Default stride is 0: pass
+
+Double list, no pairs:
+[100, 500]Initial number:      pass
+[100, 500]getIndexPair():      pass
+[100, 500]Lastupdate is 0:     pass
+[100, 500]Default stride is 0: pass
+
+Double list, no pairs:
+[100, 1000]Initial number:      pass
+[100, 1000]getIndexPair():      pass
+[100, 1000]Lastupdate is 0:     pass
+[100, 1000]Default stride is 0: pass
+
+Double list, no pairs:
+[100, 10000]Initial number:      pass
+[100, 10000]getIndexPair():      pass
+[100, 10000]Lastupdate is 0:     pass
+[100, 10000]Default stride is 0: pass
+
+Single list:
+[500]Initial number:      pass
+[500]getIndexPair():      pass
+[500]Lastupdate is 0:     pass
+[500]Default stride is 0: pass
+
+Double list, no pairs:
+[500, 100]Initial number:      pass
+[500, 100]getIndexPair():      pass
+[500, 100]Lastupdate is 0:     pass
+[500, 100]Default stride is 0: pass
+
+Double list, no pairs:
+[500, 500]Initial number:      pass
+[500, 500]getIndexPair():      pass
+[500, 500]Lastupdate is 0:     pass
+[500, 500]Default stride is 0: pass
+
+Double list, with pairs:
+[500, 500]Initial number:      pass
+[500, 500]getIndexPair():      pass
+[500, 500]Lastupdate is 0:     pass
+[500, 500]Default stride is 0: pass
+
+Double list, no pairs:
+[500, 1000]Initial number:      pass
+[500, 1000]getIndexPair():      pass
+[500, 1000]Lastupdate is 0:     pass
+[500, 1000]Default stride is 0: pass
+
+Double list, no pairs:
+[500, 10000]Initial number:      pass
+[500, 10000]getIndexPair():      pass
+[500, 10000]Lastupdate is 0:     pass
+[500, 10000]Default stride is 0: pass
+
+Single list:
+[1000]Initial number:      pass
+[1000]getIndexPair():      pass
+[1000]Lastupdate is 0:     pass
+[1000]Default stride is 0: pass
+
+Double list, no pairs:
+[1000, 100]Initial number:      pass
+[1000, 100]getIndexPair():      pass
+[1000, 100]Lastupdate is 0:     pass
+[1000, 100]Default stride is 0: pass
+
+Double list, no pairs:
+[1000, 500]Initial number:      pass
+[1000, 500]getIndexPair():      pass
+[1000, 500]Lastupdate is 0:     pass
+[1000, 500]Default stride is 0: pass
+
+Double list, no pairs:
+[1000, 1000]Initial number:      pass
+[1000, 1000]getIndexPair():      pass
+[1000, 1000]Lastupdate is 0:     pass
+[1000, 1000]Default stride is 0: pass
+
+Double list, with pairs:
+[1000, 1000]Initial number:      pass
+[1000, 1000]getIndexPair():      pass
+[1000, 1000]Lastupdate is 0:     pass
+[1000, 1000]Default stride is 0: pass
+
+Double list, no pairs:
+[1000, 10000]Initial number:      pass
+[1000, 10000]getIndexPair():      pass
+[1000, 10000]Lastupdate is 0:     pass
+[1000, 10000]Default stride is 0: pass
+
+Single list:
+[10000]Initial number:      pass
+[10000]getIndexPair():      pass
+[10000]Lastupdate is 0:     pass
+[10000]Default stride is 0: pass
+
+Double list, no pairs:
+[10000, 100]Initial number:      pass
+[10000, 100]getIndexPair():      pass
+[10000, 100]Lastupdate is 0:     pass
+[10000, 100]Default stride is 0: pass
+
+Double list, no pairs:
+[10000, 500]Initial number:      pass
+[10000, 500]getIndexPair():      pass
+[10000, 500]Lastupdate is 0:     pass
+[10000, 500]Default stride is 0: pass
+
+Double list, no pairs:
+[10000, 1000]Initial number:      pass
+[10000, 1000]getIndexPair():      pass
+[10000, 1000]Lastupdate is 0:     pass
+[10000, 1000]Default stride is 0: pass
+
+Double list, no pairs:
+[10000, 10000]Initial number:      pass
+[10000, 10000]getIndexPair():      pass
+[10000, 10000]Lastupdate is 0:     pass
+[10000, 10000]Default stride is 0: pass
+
+Double list, with pairs:
+[10000, 10000]Initial number:      pass
+[10000, 10000]getIndexPair():      pass
+[10000, 10000]Lastupdate is 0:     pass
+[10000, 10000]Default stride is 0: pass
+

regtest/basic/rt-NeigbourlistInitializationError/Makefile

@@ -0,0 +1 @@
+include ../../scripts/test.make

regtest/basic/rt-NeigbourlistInitializationError/config

@@ -0,0 +1,10 @@
+type=make
+
+plumed_regtest_after(){
+  #this discards the lines like
+  #"(tools/NeighborList.cpp:98) void PLMD::NeighborList::initialize()"
+  # in this way if NeighborList.cpp is moved or modified this test won't 
+  #trigger a (false) error
+  awk '/(Single|Double|neighbor) list/{print} 
+       /Exception text/{print}' ./unitTest > unitTest.proc
+}