Merge branch 'master' into Schwenke_numerical

PHOTOX · Mar 11, 2024 · 431080d · 431080d
2 parents de057a3 + 2b6a0b3
commit 431080d
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diff --git a/.fprettify.rc b/.fprettify.rc
@@ -26,4 +26,4 @@ enable-decl=True
 disable-fypp=True
 
 case=[1,1,1,2]
-exclude=[random.F90,fftw3.F90,force_cp2k.F90, h2o_schwenke.f]
+exclude=[random.F90,fftw3.F90,force_cp2k.F90, h2o_schwenke.f, h2o_cvrqd.f]
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,12 @@
+---
+version: 2
+updates:
+# Maintain dependencies for GitHub Actions
+    - package-ecosystem: github-actions
+      directory: /
+      schedule:
+          interval: monthly
+      groups:
+          gha-dependencies:
+              patterns:
+                  - '*'
diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml
@@ -14,10 +14,6 @@ env:
   ABIN_FFLAGS: -O0 -fopenmp --coverage -fprofile-abs-path -ffpe-trap=invalid,zero,overflow,denormal -fimplicit-none -Wall -Wno-integer-division -Wno-maybe-uninitialized
   ABIN_LDLIBS: --coverage
   OPTIMIZED_FFLAGS: -O3 -fopenmp -fimplicit-none -Wall -Wno-integer-division
-  # Even for public builds, it is apparently useful to use CODECOV_TOKEN
-  # to minimize failed uploads, see:
-  # https://community.codecov.com/t/upload-issues-unable-to-locate-build-via-github-actions-api/3954
-  # NOTE: This breaks CI on PRs from forks. We might need to change this if it becomes an issue.
   # NOTE: It would be safer to only pass the secret token to the codecov-upload action,
   # but the impact of this token leaking is small anyway.
   # NOTE: It appears that even with this token there are issues,
@@ -85,11 +81,12 @@ jobs:
     # pFUnit library is used to build and run unit tests
     - name: pFUnit build Cache
       id: pfunit-cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/pfunit/build/installed
         # To force a pFUnit rebuild (bust the cache), make a change to install_pfunit.sh
         key: ${{ runner.os }}-ubuntu20.04-pfunit-gfortran${{ env.GCC_V }}-${{ hashFiles('dev_scripts/install_pfunit.sh') }}
+        save-always: true
 
     - name: Download and build pFUnit
       if: steps.pfunit-cache.outputs.cache-hit != 'true'
@@ -105,23 +102,21 @@ jobs:
       run: make unittest
 
     - name: Codecov upload unit tests
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         name: ${{env.CODECOV_NAME}}
         flags: unittests
-        gcov: true
-        fail_ci_if_error: false
+        fail_ci_if_error: true
 
     - name: Run End-to-End tests
       if: always()
       run: make e2etest
 
     - name: Codecov upload
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         name: ${{env.CODECOV_NAME}}
-        fail_ci_if_error: false
-        gcov: true
+        fail_ci_if_error: true
 
   intel_build:
     name: Intel OneAPI build
@@ -181,7 +176,7 @@ jobs:
 
     - name: TCBP build cache
       id: tcpb-cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/tcpb-cpp/lib
         # To force a rebuild (bust the cache), make a change to install_tcpb.sh
@@ -201,11 +196,10 @@ jobs:
       run: make e2etest
 
     - name: Codecov upload
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         name: tcpb
-        fail_ci_if_error: false
-        gcov: true
+        fail_ci_if_error: true
 
 
   optimized_build:
@@ -233,10 +227,11 @@ jobs:
 
     - name: pFUnit build Cache
       id: pfunit-cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/pfunit/build/installed
         key: ${{ runner.os }}-ubuntu22.04-pfunit-gfortran${{ env.GCC_V }}-${{ hashFiles('dev_scripts/install_pfunit.sh') }}
+        save-always: true
 
     - name: Download and build pFUnit
       if: steps.pfunit-cache.outputs.cache-hit != 'true'
@@ -271,10 +266,11 @@ jobs:
 
     - name: pFUnit build Cache
       id: pfunit-cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/pfunit/build/installed
         key: ${{ runner.os }}-ubuntu22.04-pfunit-gfortran-default-${{ hashFiles('dev_scripts/install_pfunit.sh') }}
+        save-always: true
 
     - name: Download and build pFUnit
       if: steps.pfunit-cache.outputs.cache-hit != 'true'
@@ -290,21 +286,19 @@ jobs:
       run: make unittest
 
     - name: Codecov upload unit tests
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         name: ${{env.CODECOV_NAME}}
         flags: unittests
-        gcov: true
 
     - name: Run End-to-End tests
       run: make e2etest
 
     - name: Codecov upload
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         name: ${{env.CODECOV_NAME}}
-        fail_ci_if_error: false
-        gcov: true
+        fail_ci_if_error: true
 
   mpich_build:
     name: MPICH build
@@ -341,10 +335,11 @@ jobs:
         --slave /usr/bin/gcov gcov /usr/bin/gcov-${GCC_V}
     - name: MPICH build Cache
       id: mpich-cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/mpich/${{ env.MPICH_V }}/install
         key: ${{runner.os}}-ubuntu20.04-mpich${{ env.MPICH_V }}-gfortran${{ env.GCC_V }}-${{hashFiles('dev_scripts/install_mpich.sh')}}
+        save-always: true
 
     - name: Build and Install MPICH
       if: steps.mpich-cache.outputs.cache-hit != 'true'
@@ -369,11 +364,10 @@ jobs:
     - name: test ABIN
       run: make test
     - name: Codecov upload
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         name: ${{env.CODECOV_NAME}}
-        fail_ci_if_error: false
-        gcov: true
+        fail_ci_if_error: true
 
   openmpi_build:
     name: OpenMPI build
@@ -395,10 +389,11 @@ jobs:
         fetch-depth: 2
     - name: OpenMPI build cache
       id: openmpi-cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/openmpi/${{ env.OPENMPI_V }}/install
         key: ${{runner.os}}-ubuntu20.04-openmpi${{ env.OPENMPI_V }}-gfortran-default-${{hashFiles('dev_scripts/install_openmpi.sh')}}
+        save-always: true
 
     - name: Build and Install OpenMPI
       if: steps.openmpi-cache.outputs.cache-hit != 'true'
@@ -412,11 +407,10 @@ jobs:
     - name: test ABIN
       run: make test
     - name: Codecov upload
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         name: ${{env.CODECOV_NAME}}
-        fail_ci_if_error: false
-        gcov: true
+        fail_ci_if_error: true
 
   plumed_build:
     name: PLUMED build
@@ -440,18 +434,19 @@ jobs:
         fetch-depth: 2
     - name: Plumed build cache
       id: plumed-cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/plumed/${{ env.PLUMED_V }}/install
         key: ${{runner.os}}-ubuntu20.04-plumed${{env.PLUMED_V}}-gcc-default-${{hashFiles('dev_scripts/install_plumed.sh')}}
+        save-always: true
 
     - name: Build and Install PLUMED
       if: steps.plumed-cache.outputs.cache-hit != 'true'
       run: ./dev_scripts/install_plumed.sh ${HOME}/plumed ${PLUMED_V}
 
     - name: pFUnit build Cache
       id: pfunit-cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/pfunit/build/installed
         key: ${{ runner.os }}-ubuntu20.04-pfunit-gfortran-default-${{ hashFiles('dev_scripts/install_pfunit.sh') }}
@@ -473,18 +468,16 @@ jobs:
       run: make unittest
 
     - name: Codecov upload unit tests
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         name: ${{env.CODECOV_NAME}}
         flags: unittests
-        gcov: true
 
     - name: Run End-to-End tests
       run: make e2etest
 
     - name: Codecov upload
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         name: ${{env.CODECOV_NAME}}
-        fail_ci_if_error: false
-        gcov: true
+        fail_ci_if_error: true
diff --git a/src/Makefile b/src/Makefile
@@ -1,6 +1,6 @@
 F_OBJS := constants.o fortran_interfaces.o error.o modules.o mpi_wrapper.o files.o utils.o io.o random.o arrays.o qmmm.o fftw_interface.o \
           shake.o nosehoover.o gle.o transform.o potentials.o force_spline.o estimators.o ekin.o vinit.o plumed.o \
-          remd.o force_bound.o water.o h2o_schwenke.o force_h2o.o force_cp2k.o sh_integ.o surfacehop.o landau_zener.o\
+          remd.o force_bound.o water.o h2o_schwenke.o h2o_cvrqd.o force_h2o.o force_cp2k.o sh_integ.o surfacehop.o landau_zener.o\
           force_mm.o tera_mpi_api.o force_abin.o force_tcpb.o force_tera.o force_terash.o en_restraint.o analyze_ext_template.o geom_analysis.o analysis.o \
           minimizer.o mdstep.o forces.o cmdline.o init.o
 

diff --git a/src/force_h2o.F90 b/src/force_h2o.F90
@@ -57,6 +57,9 @@ subroutine force_h2o(x, y, z, fx, fy, fz, eclas, natom, nbeads)
       ! TODO: Use function pointers to select the potential and pass it down
       if (h2opot == 'schwenke') then
          call force_h2o_schwenke(x, y, z, fx, fy, fz, eclas, natom, nbeads)
+      else if (h2opot == 'cvrqd') then
+         call force_h2o_cvrqd(x, y, z, fx, fy, fz, eclas, natom, nbeads)
+         call fatal_error(__FILE__, __LINE__, 'Numerical forces not yet implemented!')
       else
          call fatal_error(__FILE__, __LINE__, 'Potential '//trim(h2opot)//' not implemented')
       end if
@@ -96,6 +99,39 @@ subroutine force_h2o_schwenke(x, y, z, fx, fy, fz, Eclas, natom, nbeads)
 
    end subroutine force_h2o_schwenke
 
+   subroutine force_h2o_cvrqd(x, y, z, fx, fy, fz, Eclas, natom, nbeads)
+      real(DP), intent(in) :: x(:, :), y(:, :), z(:, :)
+      real(DP), intent(inout) :: fx(:, :), fy(:, :), fz(:, :)
+      real(DP), intent(inout) :: Eclas
+      integer, intent(in) :: natom, nbeads
+      ! Internal water coordinates
+      real(DP) :: rOH1, rOH2, aHOH_rad
+      real(DP) :: E
+      integer :: iw
+      real(DP) :: mH, mO
+
+      ! TODO: Pass in the actual masses
+      ! What should be these set to? Should we set pure isotopes?
+      mH = 1.008D0
+      mO = 15.999D0
+
+      Eclas = 0.0D0
+      ! The H2O potentials are evaluated in internal coordinates, but ABIN works in cartesians
+      do iw = 1, nbeads
+         call get_internal_coords(x, y, z, iw, rOH1, rOH2, aHOH_rad)
+
+         call h2o_pot_cvrqd(E, rOH1, rOH2, aHOH_rad, mO, mH)
+
+         Eclas = Eclas + E
+      end do
+      Eclas = Eclas / nbeads
+
+      ! TODO: Given the small difference between the Schwenke potential,
+      ! we might not need to implement numerical forces here.
+      ! call numerical_forces(x, y, z, fx, fy, fz, Epot, natom, nbeads)
+
+   end subroutine force_h2o_cvrqd
+
    ! TODO: Implement numerical forces generally for all potentials
    ! For now, they can be implemented here and hardcoded for a specific H2O potential
    subroutine numerical_forces(x, y, z, fx, fy, fz, Epot, natom, nbeads)

diff --git a/src/fortran_interfaces.F90 b/src/fortran_interfaces.F90
@@ -63,14 +63,21 @@ function usleep(useconds) bind(c, name='usleep')
          integer(kind=C_INT) :: usleep
       end function usleep
 
-      ! Returns a potential energy of a water molecule
+      ! Computes potential energy of a water molecule
       ! using Schwenke potential, see h2o_schwenke.f
       subroutine h2o_pot_schwenke(rij, v, n)
          import :: DP
          integer, intent(in) :: n
-         real(DP) :: rij(n, 3), v(n)
+         real(DP), intent(in) :: rij(n, 3)
+         real(DP), intent(out) :: v(n)
       end subroutine h2o_pot_schwenke
 
+      subroutine h2o_pot_cvrqd(V, rOH1, rOH2, aHOH, mH, mO)
+         import :: DP
+         real(DP), intent(out) :: V
+         real(DP), intent(in) :: rOH1, rOH2, aHOH, mH, mO
+      end subroutine h2o_pot_cvrqd
+
    end interface
 
 end module mod_interfaces