From a1625482bfb36caa5d2ad6293e81d4ca40b834c0 Mon Sep 17 00:00:00 2001 From: Jiri Janos Date: Thu, 6 Apr 2023 17:43:41 +0200 Subject: [PATCH 01/61] LZ hopping probabily evaluated only to neighbouring states Current implementation allows for hops like (05-->01), which is not compatible with the LZ formula that was derived for two-state problem. This commit changes it and evaluates it only for closest neighbours. --- src/landau_zener.F90 | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/landau_zener.F90 b/src/landau_zener.F90 index 1ef54e71..8fc38904 100644 --- a/src/landau_zener.F90 +++ b/src/landau_zener.F90 @@ -175,7 +175,10 @@ subroutine lz_hop(x, y, z, vx, vy, vz, fxc, fyc, fzc, amt, dt, eclas, chpot) end if do ist1 = ibeg, iend - if (ist1 == ist) cycle + if (ist1 == ist) cycle + ! only closest states are considered for hopping + if (ist1 > (ist + 1) .or. ist1 < (ist - 1)) cycle + do ihist = 1, 3 en_diff(ihist) = abs(en_array_lz(ist, ihist) - en_array_lz(ist1, ihist)) end do From 854a96745d9302f086cd1b8d42ccbf57932d5e2d Mon Sep 17 00:00:00 2001 From: Jiri Janos Date: Wed, 12 Apr 2023 08:58:35 +0200 Subject: [PATCH 02/61] Warning for discontinuities in Landau Zener LZSH exhibits large problems when discontinuities in energies are encountered. Simple warning based on large change in second derivatives is added. It was tested on azobenzene and bilirubin and it was able to warn when suspicious hops occured. Also warning about too many states was added at the beginning of the output file. --- src/abin.F90 | 8 +- src/force_abin.F90 | 1 + src/force_terash.F90 | 1 + src/landau_zener.F90 | 36 +- tests/LZ_SS/restart.xyz.ref | 2603 ++++++++++++++++----------------- tests/LZ_ST/restart.xyz.ref | 2621 +++++++++++++++++----------------- tests/LZ_ST/stateall.dat.ref | 20 +- 7 files changed, 2663 insertions(+), 2627 deletions(-) diff --git a/src/abin.F90 b/src/abin.F90 index 83df4b25..d1bea241 100644 --- a/src/abin.F90 +++ b/src/abin.F90 @@ -25,7 +25,7 @@ program abin & nwrite, nstep, ncalc, it, inormalmodes, istage, irest use mod_init, only: init use mod_sh, only: surfacehop, sh_init, get_nacm, move_vars - use mod_lz, only: lz_hop, en_array_lz, lz_rewind + use mod_lz, only: lz_hop, en_array_lz, lz_rewind, nsinglet_lz, ntriplet_lz use mod_kinetic, only: temperature use mod_utils, only: del_file, archive_file use mod_transform, only: initialize_pi_transforms, & @@ -68,6 +68,12 @@ program abin write (stdout, '(A)') 'Job started at: '//trim(get_formatted_date_and_time(time_start)) write (stdout, *) '' + ! LZ warning for too many states + if (ipimd == 5 .and. (nsinglet_lz > 2 .or. ntriplet_lz > 2 )) then + write (*, *) 'WARNING: LZ was derived for a two-state problem. More states might cause unphysical behavior.' + write (stdout, *) '' + end if + ! Transform coordinates and velocities for Path Integral MD ! (staging or normal modes) if (istage == 1 .or. inormalmodes > 0) then diff --git a/src/force_abin.F90 b/src/force_abin.F90 index e7512971..26d03f0c 100644 --- a/src/force_abin.F90 +++ b/src/force_abin.F90 @@ -300,6 +300,7 @@ subroutine force_abin(x, y, z, fx, fy, fz, eclas, chpot, walkmax) else if (ipimd == 5) then ! Move old energies by 1 + en_array_lz(:, 4) = en_array_lz(:, 3) en_array_lz(:, 3) = en_array_lz(:, 2) en_array_lz(:, 2) = en_array_lz(:, 1) diff --git a/src/force_terash.F90 b/src/force_terash.F90 index d8a44af4..9553067a 100644 --- a/src/force_terash.F90 +++ b/src/force_terash.F90 @@ -75,6 +75,7 @@ subroutine receive_terash(fx, fy, fz, eclas, tc_comm) ! Landau-Zener arrays if (ipimd == 5) then !Move old energies by 1 + en_array_lz(:, 4) = en_array_lz(:, 3); en_array_lz(:, 3) = en_array_lz(:, 2); en_array_lz(:, 2) = en_array_lz(:, 1); !Store the new one diff --git a/src/landau_zener.F90 b/src/landau_zener.F90 index 8fc38904..6f517985 100644 --- a/src/landau_zener.F90 +++ b/src/landau_zener.F90 @@ -90,7 +90,7 @@ subroutine lz_init(pot) end do !Allocate energy arrays - allocate (en_array_lz(nstate_lz, 3), en_array_lz_backup(nstate_lz, 3)) !last 3 energies (1: current, 2: n-1, 3: n-3) + allocate (en_array_lz(nstate_lz, 4), en_array_lz_backup(nstate_lz, 4)) !last 3 energies (1: current, 2: n-1, 3: n-3) allocate (fx_old(natom, nwalk), fy_old(natom, nwalk), fz_old(natom, nwalk)) allocate (px_temp(natom, nwalk), py_temp(natom, nwalk), pz_temp(natom, nwalk)) allocate (x_prev(natom, nwalk), y_prev(natom, nwalk), z_prev(natom, nwalk), & @@ -143,7 +143,7 @@ subroutine lz_hop(x, y, z, vx, vy, vz, fxc, fyc, fzc, amt, dt, eclas, chpot) real(DP) :: prob(nstate_lz), prob2(nstate_lz), probc real(DP) :: ran(10) - real(DP) :: en_diff(3), second_der, soc_matrix(nsinglet_lz, ntriplet_lz) + real(DP) :: en_diff(4), second_der, second_der_back, der_check, soc_matrix(nsinglet_lz, ntriplet_lz) integer :: ihop, icross, ihist, ist1, iat, ibeg, iend !, istatus integer :: S_to_T !itest, iost integer :: ist ! =istate_lz @@ -178,10 +178,14 @@ subroutine lz_hop(x, y, z, vx, vy, vz, fxc, fyc, fzc, amt, dt, eclas, chpot) if (ist1 == ist) cycle ! only closest states are considered for hopping if (ist1 > (ist + 1) .or. ist1 < (ist - 1)) cycle - - do ihist = 1, 3 + + do ihist = 1, 4 en_diff(ihist) = abs(en_array_lz(ist, ihist) - en_array_lz(ist1, ihist)) end do + + ! the energy condition is considered here, otherwise it messes up probabilities + if (abs(en_diff(2) * AUTOEV) > deltaE_lz) cycle + ! Three point minima of adiabatic splitting Zjk if ((en_diff(1) > en_diff(2)) .and. (en_diff(2) < en_diff(3)) .and. (it > 2)) then second_der = ((en_diff(3) - 2 * en_diff(2) + en_diff(1)) / dt**2) @@ -195,9 +199,24 @@ subroutine lz_hop(x, y, z, vx, vy, vz, fxc, fyc, fzc, amt, dt, eclas, chpot) call fatal_error(__FILE__, __LINE__, 'LZ probability > 1') end if + ! Adding check for false 3P-minima + ! only for significant probabilities, for tiny probabilities this does not make sense + ! e.g. for parallel states (the whole LZ does not make sense for this case) + if (prob(ist1) > 0.01) then + second_der_back = ((en_diff(2) - 2 * en_diff(3) + en_diff(4)) / dt**2) + der_check = abs((second_der - second_der_back) / second_der) + if (der_check > 0.3) then + write (*,*) "WARNING, possible discontinuity in PES! Check PES.dat!" + end if + end if + end if end do - !write(stdout,*) "diff1",en_diff(1),"diff2",en_diff(2),"diff3",en_diff(3) + + ! LZ warning + if (sum(prob) > 1) then + write (*,*) "* WARNING, sum of hopping probabilities > 1. Breakdown of LZ assumptions" + end if !Hop? ihop = 0 @@ -234,7 +253,7 @@ subroutine lz_hop(x, y, z, vx, vy, vz, fxc, fyc, fzc, amt, dt, eclas, chpot) if (ihop /= 0) then Ekin = ekin_v(vx, vy, vz) dE = (en_array_lz(ihop, 2) - en_array_lz(ist, 2)) - Epot = abs(en_array_lz(ist, 1) - en_array_lz(ihop, 1)) + Epot = abs(en_array_lz(ist, 1) - en_array_lz(ihop, 1)) ! This is not used anywhere in the code Epot2 = abs(en_array_lz(ist, 2) - en_array_lz(ihop, 2)) write (fmt_in, '(I2.2)') istate_lz write (fmt_out, '(I2.2)') ihop @@ -285,6 +304,7 @@ subroutine lz_hop(x, y, z, vx, vy, vz, fxc, fyc, fzc, amt, dt, eclas, chpot) !e) Update only last energy history entry en_array_lz(:, 2) = en_array_lz_backup(:, 2) en_array_lz(:, 3) = en_array_lz_backup(:, 3) + en_array_lz(:, 4) = en_array_lz_backup(:, 4) else write (stdout, *) "NO adiabatic HOP (", trim(fmt_in), "->", trim(fmt_out), ")dE/a.u.", Epot2, & @@ -556,7 +576,7 @@ subroutine lz_restout(fileunit) write (fileunit, *) istate_lz do ist = 1, nstate_lz - write (fileunit, '(3ES25.16E3)') en_array_lz(ist, 1), en_array_lz(ist, 2), en_array_lz(ist, 3) + write (fileunit, '(3ES25.16E3)') en_array_lz(ist, 1), en_array_lz(ist, 2), en_array_lz(ist, 3), en_array_lz(ist, 4) end do end subroutine lz_restout @@ -584,7 +604,7 @@ subroutine lz_restin(fileunit, x, y, z, vx, vy, vz) end if do ist = 1, nstate_lz - read (fileunit, *) en_array_lz(ist, 1), en_array_lz(ist, 2), en_array_lz(ist, 3) + read (fileunit, *) en_array_lz(ist, 1), en_array_lz(ist, 2), en_array_lz(ist, 3), en_array_lz(ist, 4) end do !Store previous step values diff --git a/tests/LZ_SS/restart.xyz.ref b/tests/LZ_SS/restart.xyz.ref index 269b1f71..e787a7ed 100644 --- a/tests/LZ_SS/restart.xyz.ref +++ b/tests/LZ_SS/restart.xyz.ref @@ -1,1306 +1,1309 @@ - 10 100.00000000000000 +10 1.0000000000000000E+002 Cartesian Coordinates [au] - -1.9364324259617078 -2.6605292764925466 -0.10224417442984338 - 0.86997754122248017 1.8901712905272237 1.8207823291854579 - -0.76329981664742508 -3.4963405866520754 -1.2168279443797034 - -3.0492007055536154 -1.2311514676572006 0.92861134409524548 - 2.1011884380249390 0.61690339979383801 2.3652616421347288 - 2.6883938075810634 2.6243408598405322 0.52608370645489433 + -1.9364324259617078E+000 -2.6605292764925466E+000 -1.0224417442984338E-001 + 8.6997754122248017E-001 1.8901712905272237E+000 1.8207823291854579E+000 + -7.6329981664742508E-001 -3.4963405866520754E+000 -1.2168279443797034E+000 + -3.0492007055536154E+000 -1.2311514676572006E+000 9.2861134409524548E-001 + 2.1011884380249390E+000 6.1690339979383801E-001 2.3652616421347288E+000 + 2.6883938075810634E+000 2.6243408598405322E+000 5.2608370645489433E-001 Cartesian Velocities [au] - -6.2541331318772945E-004 -1.7186982965908355E-003 -3.0636402554938660E-004 - 2.7528787990875413E-004 7.9328082231737386E-004 7.1632940330620780E-004 - 1.8493150786253330E-004 3.3111172738813826E-003 5.4067050942694283E-004 - -1.0103552429958959E-003 4.3434957130716679E-003 -1.8806176502816256E-003 - 5.8628716364069898E-004 2.2733862602508252E-004 -3.8094988094623606E-003 - 3.8660035998388060E-003 1.5741999368462552E-003 -1.1540140006298522E-003 + -6.2541331318772945E-004 -1.7186982965908355E-003 -3.0636402554938660E-004 + 2.7528787990875413E-004 7.9328082231737386E-004 7.1632940330620780E-004 + 1.8493150786253330E-004 3.3111172738813826E-003 5.4067050942694283E-004 + -1.0103552429958959E-003 4.3434957130716679E-003 -1.8806176502816256E-003 + 5.8628716364069898E-004 2.2733862602508252E-004 -3.8094988094623606E-003 + 3.8660035998388060E-003 1.5741999368462552E-003 -1.1540140006298522E-003 Energy difference history for LZ 2 - -94.089625847768389 -94.089734388134346 -94.089721321419489 - -94.084269652748361 -94.085985079607525 -94.087433859349289 - -93.999270951262247 -93.999358990659246 -93.999541872297826 + -9.4089625847768389E+001 -9.4089734388134346E+001 -9.4089721321419489E+001 + -9.4089611644167093E+001 + -9.4084269652748361E+001 -9.4085985079607525E+001 -9.4087433859349289E+001 + -9.4088568320312035E+001 + -9.3999270951262247E+001 -9.3999358990659246E+001 -9.3999541872297826E+001 + -9.3999788225478142E+001 Cumulative averages of various estimators - 0.10362047031511409 - 0.0000000000000000 0.0000000000000000 - 0.0000000000000000 + 1.0362047031511409E-001 + 0.0000000000000000E+000 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6.6747311553403676E-001 + 8.1888736102110471E-001 + 5.5066140055160062E-001 + 5.3259879758453366E-002 + 6.0000857598011947E-001 + 6.8408604414470986E-001 + 4.1953733169475171E-001 + 6.9324589696984518E-001 + 2.8715731261234012E-001 + 9.4738928933217181E-001 + 2.5792224939820585E-002 + 6.7017908357997769E-001 + 9.8836347760420651E-001 + 6.0750483689547963E-001 + 1.4125816059064178E-001 diff --git a/tests/LZ_ST/stateall.dat.ref b/tests/LZ_ST/stateall.dat.ref index 5ba122bf..6756cc81 100644 --- a/tests/LZ_ST/stateall.dat.ref +++ b/tests/LZ_ST/stateall.dat.ref @@ -1,15 +1,15 @@ timestep: 0 - 5 - 4 +5 +4 timestep: 1 - 5 - 4 +5 +4 timestep: 2 - 5 - 4 +5 +4 timestep: 2 - 5 - 2 +5 +2 timestep: 3 - 5 - 2 +5 +2 From 14749f6cf4c851804b1ebb9d22a4e8d39d7f2d36 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 14:45:33 +0100 Subject: [PATCH 03/61] GHA: Update Ubuntu version to 20.04 This unfortunately means we can no longer test with gfortran-7. --- .github/workflows/gfortran.yml | 49 +++++++++++----------------------- 1 file changed, 16 insertions(+), 33 deletions(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index e97cb9f4..f0cf9da8 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -15,11 +15,11 @@ jobs: basic_build: name: Basic build - runs-on: ubuntu-18.04 + runs-on: ubuntu-20.04 strategy: fail-fast: false matrix: - gcc_v: [7, 9, 10] + gcc_v: [9, 10, 11] env: FC: gfortran GCC_V: ${{ matrix.gcc_v}} @@ -119,8 +119,6 @@ jobs: tcpb_build: name: TCPB build - # NOTE: tcpb-cpp fails to build on Ubuntu 18.04, - # probably because of old libprotobuf library? runs-on: ubuntu-20.04 needs: basic_build env: @@ -167,11 +165,11 @@ jobs: optimized_build: name: Optimized build - runs-on: ubuntu-18.04 + runs-on: ubuntu-20.04 needs: basic_build strategy: matrix: - gcc_v: [7, 9, 10] + gcc_v: [8, 9, 10] env: FC: gfortran GCC_V: ${{ matrix.gcc_v}} @@ -215,16 +213,13 @@ jobs: # However, some tests started to fail, with small numerical differences ~1E-15. # Not sure why, since default gfortran on 20.04 is 9.3.0, i.e. the same as we already # test above. I tested this with both -O0 and -O2. - runs-on: ubuntu-18.04 + runs-on: ubuntu-20.04 name: FFTW build needs: basic_build strategy: fail-fast: false - matrix: - gcc_v: [7] env: - GCC_V: ${{ matrix.gcc_v}} - CODECOV_NAME: ${{format('{0} GCC-{1}', github.job, matrix.gcc_v)}} + CODECOV_NAME: ${{format('{0}', github.job)}} steps: - uses: actions/checkout@v2 with: @@ -238,7 +233,7 @@ jobs: uses: actions/cache@v2 with: path: ~/pfunit/build/installed - key: ${{ runner.os }}-pfunit-gfortran${{ env.GCC_V }}-${{ hashFiles('dev_scripts/install_pfunit.sh') }} + key: ${{ runner.os }}-pfunit-gfortran-default-${{ hashFiles('dev_scripts/install_pfunit.sh') }} - name: Download and build pFUnit if: steps.pfunit-cache.outputs.cache-hit != 'true' @@ -272,13 +267,13 @@ jobs: mpich_build: name: MPICH build - runs-on: ubuntu-18.04 + runs-on: ubuntu-20.04 timeout-minutes: 25 needs: basic_build strategy: fail-fast: false matrix: - gcc_v: [7, 10] + gcc_v: [9, 10] mpich_v: ["3.4.3", "4.0.2"] env: # To speed-up MPICH build @@ -334,21 +329,15 @@ jobs: openmpi_build: name: OpenMPI build - runs-on: ubuntu-18.04 + runs-on: ubuntu-20.04 timeout-minutes: 25 needs: basic_build strategy: fail-fast: false - # Let's just test one GFortran version, we do not really - # use OpenMPI with ABIN, and we already test all GCC - # versions with MPICH. - matrix: - gcc_v: [7] env: # To speed-up OpenMPI build CFLAGS: -O0 - GCC_V: ${{ matrix.gcc_v}} - CODECOV_NAME: ${{format('{0} GCC-{1} OpenMPI-4.0', github.job, matrix.gcc_v)}} + CODECOV_NAME: ${{format('{0} OpenMPI-4.0', github.job)}} OPENMPI_V: "4.1" OPENMPI_PATCH: "2" @@ -356,16 +345,12 @@ jobs: - uses: actions/checkout@v2 with: fetch-depth: 2 - - name: Set GFortran version - run: | - sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-${GCC_V} 100 \ - --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-${GCC_V} - name: OpenMPI build cache id: openmpi-cache uses: actions/cache@v2 with: path: ~/openmpi/${{ env.OPENMPI_V }}/install - key: ${{runner.os}}-openmpi${{ env.OPENMPI_V }}-gfortran${{ env.GCC_V }}-${{hashFiles('dev_scripts/install_openmpi.sh')}} + key: ${{runner.os}}-openmpi${{ env.OPENMPI_V }}-gfortran-default-${{hashFiles('dev_scripts/install_openmpi.sh')}} - name: Build and Install OpenMPI if: steps.openmpi-cache.outputs.cache-hit != 'true' @@ -387,21 +372,19 @@ jobs: plumed_build: name: PLUMED build - runs-on: ubuntu-18.04 + runs-on: ubuntu-20.04 needs: basic_build strategy: fail-fast: false matrix: plumed_v: [2.7.4, 2.8.0] - gcc_v: [7] env: PLUMED_V: ${{ matrix.plumed_v}} - GCC_V: ${{ matrix.gcc_v}} # Speeding up the Plumed build CFLAGS: -O0 CXXLAGS: -O0 - CODECOV_NAME: ${{format('{0} GCC-{1} PLUMED-{2}', github.job, matrix.gcc_v, matrix.plumed_v)}} + CODECOV_NAME: ${{format('{0} PLUMED-{2}', github.job, matrix.plumed_v)}} steps: - uses: actions/checkout@v2 @@ -412,7 +395,7 @@ jobs: uses: actions/cache@v2 with: path: ~/plumed/${{ env.PLUMED_V }}/install - key: ${{runner.os}}-plumed${{env.PLUMED_V}}-gcc${{ env.GCC_V }}-${{hashFiles('dev_scripts/install_plumed.sh')}} + key: ${{runner.os}}-plumed${{env.PLUMED_V}}-gcc-default-${{hashFiles('dev_scripts/install_plumed.sh')}} - name: Build and Install PLUMED if: steps.plumed-cache.outputs.cache-hit != 'true' @@ -423,7 +406,7 @@ jobs: uses: actions/cache@v2 with: path: ~/pfunit/build/installed - key: ${{ runner.os }}-pfunit-gfortran${{ env.GCC_V }}-${{ hashFiles('dev_scripts/install_pfunit.sh') }} + key: ${{ runner.os }}-pfunit-gfortran-default-${{ hashFiles('dev_scripts/install_pfunit.sh') }} - name: Download and build pFUnit if: steps.pfunit-cache.outputs.cache-hit != 'true' From 5ac7a499b230626be794b631c7756b4e1dc690b1 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 15:00:46 +0100 Subject: [PATCH 04/61] Fix gcc versions --- .github/workflows/gfortran.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index f0cf9da8..07bf739a 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -19,7 +19,7 @@ jobs: strategy: fail-fast: false matrix: - gcc_v: [9, 10, 11] + gcc_v: [9, 10] env: FC: gfortran GCC_V: ${{ matrix.gcc_v}} @@ -165,11 +165,11 @@ jobs: optimized_build: name: Optimized build - runs-on: ubuntu-20.04 + runs-on: ubuntu-22.04 needs: basic_build strategy: matrix: - gcc_v: [8, 9, 10] + gcc_v: [10, 11, 12] env: FC: gfortran GCC_V: ${{ matrix.gcc_v}} From ad668cb276073352bbe246959cf23c8d1f4f6598 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 15:16:13 +0100 Subject: [PATCH 05/61] More fixes --- .github/workflows/gfortran.yml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 07bf739a..8fbd2352 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -165,11 +165,16 @@ jobs: optimized_build: name: Optimized build + # NOTE: We use a more recent Ubuntu version here + # so we can test more recent GCC versions. + # NOTE: Because the cache key does not take into account OS version, + # we cannot test same GCC versions as in the basic build. runs-on: ubuntu-22.04 needs: basic_build strategy: + fail-fast: false matrix: - gcc_v: [10, 11, 12] + gcc_v: [11, 12] env: FC: gfortran GCC_V: ${{ matrix.gcc_v}} @@ -384,7 +389,7 @@ jobs: # Speeding up the Plumed build CFLAGS: -O0 CXXLAGS: -O0 - CODECOV_NAME: ${{format('{0} PLUMED-{2}', github.job, matrix.plumed_v)}} + CODECOV_NAME: ${{format('{0} PLUMED-{1}', github.job, matrix.plumed_v)}} steps: - uses: actions/checkout@v2 From 5d0e95ae00ac5baa903de83bb80eef9c716ca91e Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 15:18:32 +0100 Subject: [PATCH 06/61] FFTW tests seems to work now --- .github/workflows/gfortran.yml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 8fbd2352..0b540cb8 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -213,11 +213,6 @@ jobs: # Here we just take the defaults everywhere, except turning on FFTW # To use FFTW with other Gfortran versions, we would need to build it. fftw_build: - # NOTE: I tried using `ubuntu-20.04` instead of `ubuntu-18.04`. - # https://github.com/actions/virtual-environments#available-environments - # However, some tests started to fail, with small numerical differences ~1E-15. - # Not sure why, since default gfortran on 20.04 is 9.3.0, i.e. the same as we already - # test above. I tested this with both -O0 and -O2. runs-on: ubuntu-20.04 name: FFTW build needs: basic_build From f77a5314b39ad5ac58e6e1fdcddd4f75fe372468 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 15:35:24 +0100 Subject: [PATCH 07/61] include OS version in cache keys --- .github/workflows/gfortran.yml | 23 +++++++++++++---------- 1 file changed, 13 insertions(+), 10 deletions(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 0b540cb8..2ff8c190 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -1,5 +1,9 @@ name: GFortran CI +# WARNING: When updating the OS version of the Github Actions runner, +# e.g. from Ubuntu 20.04 to 22.04, you need to manually update the cache keys! +# This is because there's no easy way to get the OS version from within this workflow file. + on: push: branches: [ master ] @@ -42,7 +46,7 @@ jobs: with: path: ~/pfunit/build/installed # To force a pFUnit rebuild (bust the cache), make a change to install_pfunit.sh - key: ${{ runner.os }}-pfunit-gfortran${{ env.GCC_V }}-${{ hashFiles('dev_scripts/install_pfunit.sh') }} + key: ${{ runner.os }}-ubuntu20.04-pfunit-gfortran${{ env.GCC_V }}-${{ hashFiles('dev_scripts/install_pfunit.sh') }} - name: Download and build pFUnit if: steps.pfunit-cache.outputs.cache-hit != 'true' @@ -123,8 +127,7 @@ jobs: needs: basic_build env: FC: gfortran - GCC_V: 9 - CODECOV_NAME: ${{format('{0} GCC9', github.job)}} + CODECOV_NAME: ${{format('{0}', github.job)}} steps: - uses: actions/checkout@v2 with: @@ -139,7 +142,7 @@ jobs: with: path: ~/tcpb-cpp/lib # To force a rebuild (bust the cache), make a change to install_tcpb.sh - key: ${{ runner.os }}-tcpb-gfortran${{ env.GCC_V }}-${{ hashFiles('dev_scripts/install_tcpb.sh') }} + key: ${{ runner.os }}-ubuntu20.04-tcpb-gfortran-default-${{ hashFiles('dev_scripts/install_tcpb.sh') }} - name: Download and build tcpb_cpp if: steps.tcpb-cache.outputs.cache-hit != 'true' @@ -193,7 +196,7 @@ jobs: uses: actions/cache@v2 with: path: ~/pfunit/build/installed - key: ${{ runner.os }}-pfunit-gfortran${{ env.GCC_V }}-${{ hashFiles('dev_scripts/install_pfunit.sh') }} + key: ${{ runner.os }}-ubuntu22.04-pfunit-gfortran${{ env.GCC_V }}-${{ hashFiles('dev_scripts/install_pfunit.sh') }} - name: Download and build pFUnit if: steps.pfunit-cache.outputs.cache-hit != 'true' @@ -233,7 +236,7 @@ jobs: uses: actions/cache@v2 with: path: ~/pfunit/build/installed - key: ${{ runner.os }}-pfunit-gfortran-default-${{ hashFiles('dev_scripts/install_pfunit.sh') }} + key: ${{ runner.os }}-ubuntu20.04-pfunit-gfortran-default-${{ hashFiles('dev_scripts/install_pfunit.sh') }} - name: Download and build pFUnit if: steps.pfunit-cache.outputs.cache-hit != 'true' @@ -296,7 +299,7 @@ jobs: uses: actions/cache@v2 with: path: ~/mpich/${{ env.MPICH_V }}/install - key: ${{runner.os}}-mpich${{ env.MPICH_V }}-gfortran${{ env.GCC_V }}-${{hashFiles('dev_scripts/install_mpich.sh')}} + key: ${{runner.os}}-ubuntu20.04-mpich${{ env.MPICH_V }}-gfortran${{ env.GCC_V }}-${{hashFiles('dev_scripts/install_mpich.sh')}} - name: Build and Install MPICH if: steps.mpich-cache.outputs.cache-hit != 'true' @@ -350,7 +353,7 @@ jobs: uses: actions/cache@v2 with: path: ~/openmpi/${{ env.OPENMPI_V }}/install - key: ${{runner.os}}-openmpi${{ env.OPENMPI_V }}-gfortran-default-${{hashFiles('dev_scripts/install_openmpi.sh')}} + key: ${{runner.os}}-ubuntu20.04-openmpi${{ env.OPENMPI_V }}-gfortran-default-${{hashFiles('dev_scripts/install_openmpi.sh')}} - name: Build and Install OpenMPI if: steps.openmpi-cache.outputs.cache-hit != 'true' @@ -395,7 +398,7 @@ jobs: uses: actions/cache@v2 with: path: ~/plumed/${{ env.PLUMED_V }}/install - key: ${{runner.os}}-plumed${{env.PLUMED_V}}-gcc-default-${{hashFiles('dev_scripts/install_plumed.sh')}} + key: ${{runner.os}}-ubuntu20.04-plumed${{env.PLUMED_V}}-gcc-default-${{hashFiles('dev_scripts/install_plumed.sh')}} - name: Build and Install PLUMED if: steps.plumed-cache.outputs.cache-hit != 'true' @@ -406,7 +409,7 @@ jobs: uses: actions/cache@v2 with: path: ~/pfunit/build/installed - key: ${{ runner.os }}-pfunit-gfortran-default-${{ hashFiles('dev_scripts/install_pfunit.sh') }} + key: ${{ runner.os }}-ubuntu20.04-pfunit-gfortran-default-${{ hashFiles('dev_scripts/install_pfunit.sh') }} - name: Download and build pFUnit if: steps.pfunit-cache.outputs.cache-hit != 'true' From 802d7e338180201d23043f64c1e6b625db2efd1f Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 15:39:13 +0100 Subject: [PATCH 08/61] Update Plumed versions --- .github/workflows/gfortran.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 2ff8c190..a28d31bf 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -380,7 +380,7 @@ jobs: strategy: fail-fast: false matrix: - plumed_v: [2.7.4, 2.8.0] + plumed_v: [2.7.6, 2.8.2] env: PLUMED_V: ${{ matrix.plumed_v}} From 86a7cd1c20dcf70c0db2a9318d0874dba5edb074 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 15:52:20 +0100 Subject: [PATCH 09/61] Try if GCC9 is available in Ubuntu 22.04 --- .github/workflows/gfortran.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index a28d31bf..abec3306 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -177,7 +177,7 @@ jobs: strategy: fail-fast: false matrix: - gcc_v: [11, 12] + gcc_v: [9, 11, 12] env: FC: gfortran GCC_V: ${{ matrix.gcc_v}} From 9fa909ab0a44a242f75d1723d432b1fe3e2c5f58 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 16:37:52 +0100 Subject: [PATCH 10/61] Update actions/checkout --- .github/workflows/gfortran.yml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index abec3306..23573404 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -30,7 +30,7 @@ jobs: CODECOV_NAME: ${{format('{0} GCC-{1}', github.job, matrix.gcc_v)}} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 with: fetch-depth: 2 - name: Set GFortran version @@ -95,7 +95,7 @@ jobs: # intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 with: fetch-depth: 2 @@ -129,7 +129,7 @@ jobs: FC: gfortran CODECOV_NAME: ${{format('{0}', github.job)}} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 with: fetch-depth: 2 @@ -183,7 +183,7 @@ jobs: GCC_V: ${{ matrix.gcc_v}} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 with: fetch-depth: 2 - name: Set GFortran version @@ -224,7 +224,7 @@ jobs: env: CODECOV_NAME: ${{format('{0}', github.job)}} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 with: fetch-depth: 2 @@ -286,7 +286,7 @@ jobs: CODECOV_NAME: ${{format('{0} GCC-{1} MPICH-{2}', github.job, matrix.gcc_v, matrix.mpich_v)}} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 with: fetch-depth: 2 - name: Set GFortran version @@ -345,7 +345,7 @@ jobs: OPENMPI_PATCH: "2" steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 with: fetch-depth: 2 - name: OpenMPI build cache @@ -390,7 +390,7 @@ jobs: CODECOV_NAME: ${{format('{0} PLUMED-{1}', github.job, matrix.plumed_v)}} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 with: fetch-depth: 2 - name: Plumed build cache From d92acbc21abc952316de37c95e878e2317b5892e Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 16:41:15 +0100 Subject: [PATCH 11/61] codecov: Update number of builds --- codecov.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/codecov.yml b/codecov.yml index fbba5caf..dfab836e 100644 --- a/codecov.yml +++ b/codecov.yml @@ -5,13 +5,13 @@ codecov: # are completed, otherwise we'll temporarily receive # incomplete coverage reports. # Right now, the following builds are collecting coverage data: - # Basic Builds - (Gfortran versions 7, 8, 9) + # Basic Builds - (2) # OpenMPI Build # mpich builds (4) # FFTW Build # Intel Build # Plumed Builds (2 total) - after_n_builds: 18 + after_n_builds: 16 wait_for_ci: yes coverage: From 1df87657a2b419ce44f60bb7d0ca5c3c7ce2e98f Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 16:52:57 +0100 Subject: [PATCH 12/61] verbose codecov --- .github/workflows/gfortran.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 23573404..f700168b 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -229,7 +229,7 @@ jobs: fetch-depth: 2 - name: Install FFTW libraries - run: sudo apt-get install libfftw3-dev + run: sudo apt-get install libfftw3-dev gcov - name: pFUnit build Cache id: pfunit-cache @@ -267,6 +267,7 @@ jobs: name: ${{env.CODECOV_NAME}} fail_ci_if_error: true gcov: true + verbose: true mpich_build: name: MPICH build @@ -443,3 +444,4 @@ jobs: name: ${{env.CODECOV_NAME}} fail_ci_if_error: true gcov: true + verbose: true From 3899eae139196d392fa96b81899b28a48e41da4e Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 17:34:46 +0100 Subject: [PATCH 13/61] Trying to fix codecov gcov paths --- codecov.yml | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/codecov.yml b/codecov.yml index dfab836e..ac6bb35d 100644 --- a/codecov.yml +++ b/codecov.yml @@ -46,9 +46,14 @@ comment: require_changes: no ignore: - - "docs" - - "sample_inputs" - - "interfaces" - - "utils" - - "dev_scripts" + - "docs/*" + - "tests/*" + - "sample_inputs/*" + - "interfaces/*" + - "utils/*" + - "dev_scripts/*" + - "*.md" - "**/*.md" + +fixes: + - "::src/" From 7e0d57f3e9332b96061894f72f60c4e5ae756cf7 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 17:47:03 +0100 Subject: [PATCH 14/61] do not install gcov --- .github/workflows/gfortran.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index f700168b..29978301 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -229,7 +229,7 @@ jobs: fetch-depth: 2 - name: Install FFTW libraries - run: sudo apt-get install libfftw3-dev gcov + run: sudo apt-get install libfftw3-dev - name: pFUnit build Cache id: pfunit-cache From 42ccabf79bf448e6849c08bc764778bd941fd912 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 18:04:00 +0100 Subject: [PATCH 15/61] Run gcov manually --- .github/workflows/gfortran.yml | 19 +++++-------------- 1 file changed, 5 insertions(+), 14 deletions(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 29978301..fa97883b 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -66,7 +66,6 @@ jobs: with: name: ${{env.CODECOV_NAME}} flags: unittests - gcov: false - name: Run End-to-End tests run: make e2etest && cd src/ && gcov *.o @@ -76,8 +75,6 @@ jobs: with: name: ${{env.CODECOV_NAME}} fail_ci_if_error: true - verbose: true - gcov: false intel_build: name: Intel OneAPI build @@ -163,7 +160,6 @@ jobs: name: tcpb fail_ci_if_error: true verbose: true - gcov: false optimized_build: @@ -249,24 +245,22 @@ jobs: LDLIBS: ${{ env.ABIN_LDLIBS }} - name: Run Unit tests - run: make unittest + run: make unittest && cd src/ && gcov *.o - name: Codecov upload unit tests uses: codecov/codecov-action@v3 with: name: ${{env.CODECOV_NAME}} flags: unittests - gcov: true - name: Run End-to-End tests - run: make e2etest + run: make e2etest && cd src/ && gcov *.o - name: Codecov upload uses: codecov/codecov-action@v3 with: name: ${{env.CODECOV_NAME}} fail_ci_if_error: true - gcov: true verbose: true mpich_build: @@ -366,13 +360,12 @@ jobs: FFLAGS: ${{ env.ABIN_FFLAGS }} LDLIBS: ${{ env.ABIN_LDLIBS }} - name: test ABIN - run: make test + run: make test && cd src/ && gcov *.o - name: Codecov upload uses: codecov/codecov-action@v3 with: name: ${{env.CODECOV_NAME}} fail_ci_if_error: true - gcov: true plumed_build: name: PLUMED build @@ -426,22 +419,20 @@ jobs: LDLIBS: ${{ env.ABIN_LDLIBS }} - name: Run Unit tests - run: make unittest + run: make unittest && cd src/ && gcov *.o - name: Codecov upload unit tests uses: codecov/codecov-action@v3 with: name: ${{env.CODECOV_NAME}} flags: unittests - gcov: true - name: Run End-to-End tests - run: make e2etest + run: make e2etest && cd src/ && gcov *.o - name: Codecov upload uses: codecov/codecov-action@v3 with: name: ${{env.CODECOV_NAME}} fail_ci_if_error: true - gcov: true verbose: true From f2034d9af3a64f0c5fd81135c73f437cc0d185fa Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 18:19:51 +0100 Subject: [PATCH 16/61] Remove verbose --- .github/workflows/gfortran.yml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index fa97883b..a2b271d5 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -88,7 +88,6 @@ jobs: intel-oneapi-compiler-fortran intel-oneapi-mpi intel-oneapi-mpi-devel - # intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic steps: @@ -159,7 +158,6 @@ jobs: with: name: tcpb fail_ci_if_error: true - verbose: true optimized_build: @@ -261,7 +259,6 @@ jobs: with: name: ${{env.CODECOV_NAME}} fail_ci_if_error: true - verbose: true mpich_build: name: MPICH build @@ -323,7 +320,6 @@ jobs: with: name: ${{env.CODECOV_NAME}} fail_ci_if_error: true - gcov: false openmpi_build: name: OpenMPI build @@ -435,4 +431,3 @@ jobs: with: name: ${{env.CODECOV_NAME}} fail_ci_if_error: true - verbose: true From 8ea5179a4ad4e450b1d87ff450714978b15f8b85 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 18:26:24 +0100 Subject: [PATCH 17/61] revert codecov.yml changes that did not do anything --- codecov.yml | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/codecov.yml b/codecov.yml index ac6bb35d..81d765f9 100644 --- a/codecov.yml +++ b/codecov.yml @@ -46,14 +46,9 @@ comment: require_changes: no ignore: - - "docs/*" - - "tests/*" - - "sample_inputs/*" - - "interfaces/*" - - "utils/*" - - "dev_scripts/*" - - "*.md" + - "docs" + - "tests" + - "sample_inputs" + - "utils" + - "dev_scripts" - "**/*.md" - -fixes: - - "::src/" From b6680cc2a105f8484df21d7ff8f72957842948e5 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 18:40:27 +0100 Subject: [PATCH 18/61] simplify codecov yaml --- codecov.yml | 19 ++----------------- 1 file changed, 2 insertions(+), 17 deletions(-) diff --git a/codecov.yml b/codecov.yml index 81d765f9..48f69e06 100644 --- a/codecov.yml +++ b/codecov.yml @@ -4,13 +4,7 @@ codecov: # Send report to Github PR only after all CIs # are completed, otherwise we'll temporarily receive # incomplete coverage reports. - # Right now, the following builds are collecting coverage data: - # Basic Builds - (2) - # OpenMPI Build - # mpich builds (4) - # FFTW Build - # Intel Build - # Plumed Builds (2 total) + # Note that unit test coverage builds count towards the build count! after_n_builds: 16 wait_for_ci: yes @@ -29,8 +23,7 @@ coverage: - unittests patch: default: - target: auto - threshold: 10% + target: 80% parsers: gcov: @@ -44,11 +37,3 @@ comment: layout: "reach,diff,flags,tree" behavior: default require_changes: no - -ignore: - - "docs" - - "tests" - - "sample_inputs" - - "utils" - - "dev_scripts" - - "**/*.md" From de714922b4c7ef4ba27fc75017bff35fc023a2ca Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 18:57:12 +0100 Subject: [PATCH 19/61] Add gcov options to fix coverage? --- .github/workflows/gfortran.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index a2b271d5..8147fe3e 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -59,7 +59,7 @@ jobs: LDLIBS: ${{ env.ABIN_LDLIBS }} - name: Run Unit tests - run: make unittest && cd src/ && gcov *.o + run: make unittest && cd src/ && gcov -uba *.o - name: Codecov upload unit tests uses: codecov/codecov-action@v3 @@ -68,7 +68,7 @@ jobs: flags: unittests - name: Run End-to-End tests - run: make e2etest && cd src/ && gcov *.o + run: make e2etest && cd src/ && gcov -uba *.o - name: Codecov upload uses: codecov/codecov-action@v3 From 9af96a73b538c6167c1bb513a078a6daa2a0cbf3 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 19:06:04 +0100 Subject: [PATCH 20/61] Install gcc-7 --- .github/workflows/gfortran.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 8147fe3e..1c466728 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -23,7 +23,7 @@ jobs: strategy: fail-fast: false matrix: - gcc_v: [9, 10] + gcc_v: [7, 9, 10] env: FC: gfortran GCC_V: ${{ matrix.gcc_v}} @@ -33,6 +33,10 @@ jobs: - uses: actions/checkout@v3 with: fetch-depth: 2 + + - name: Install GCC-7 + run: sudo apt install gcc-7 + - name: Set GFortran version run: | sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-${GCC_V} 100 \ From 5794619933ccf33cc787af5c0d372bbea1c3c5b1 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 19:13:31 +0100 Subject: [PATCH 21/61] Try again --- .github/workflows/gfortran.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 1c466728..69b93376 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -35,7 +35,7 @@ jobs: fetch-depth: 2 - name: Install GCC-7 - run: sudo apt install gcc-7 + run: sudo apt install gcc-7 gfortran-7 - name: Set GFortran version run: | From 2ab40ba47a14d37618ae4aa1cf1eac002e861ebf Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 19:25:32 +0100 Subject: [PATCH 22/61] Use gcov args as in codecov --- .github/workflows/gfortran.yml | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 69b93376..ba7b787a 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -14,6 +14,9 @@ env: ABIN_FFLAGS: -O0 -fopenmp --coverage -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 + # These are the defaults used in Codecov, see: + # https://github.com/codecov/uploader/blob/main/src/helpers/gcov.ts + GCOV_ARGS: -pb jobs: @@ -63,7 +66,7 @@ jobs: LDLIBS: ${{ env.ABIN_LDLIBS }} - name: Run Unit tests - run: make unittest && cd src/ && gcov -uba *.o + run: make unittest && cd src/ && gcov ${GCOV_ARGS} *.o - name: Codecov upload unit tests uses: codecov/codecov-action@v3 @@ -72,7 +75,7 @@ jobs: flags: unittests - name: Run End-to-End tests - run: make e2etest && cd src/ && gcov -uba *.o + run: make e2etest && cd src/ && gcov ${GCOV_ARGS} *.o - name: Codecov upload uses: codecov/codecov-action@v3 @@ -155,7 +158,7 @@ jobs: LDLIBS: ${{ env.ABIN_LDLIBS }} - name: Run End-to-End tests - run: make e2etest && cd src/ && gcov *.o + run: make e2etest && cd src/ && gcov ${GCOV_ARGS} *.o - name: Codecov upload uses: codecov/codecov-action@v3 @@ -247,7 +250,7 @@ jobs: LDLIBS: ${{ env.ABIN_LDLIBS }} - name: Run Unit tests - run: make unittest && cd src/ && gcov *.o + run: make unittest && cd src/ && gcov ${GCOV_ARGS} *.o - name: Codecov upload unit tests uses: codecov/codecov-action@v3 @@ -256,7 +259,7 @@ jobs: flags: unittests - name: Run End-to-End tests - run: make e2etest && cd src/ && gcov *.o + run: make e2etest && cd src/ && gcov ${GCOV_ARGS} *.o - name: Codecov upload uses: codecov/codecov-action@v3 @@ -318,7 +321,7 @@ jobs: FFLAGS: ${{ env.ABIN_FFLAGS }} -g LDLIBS: ${{ env.ABIN_LDLIBS }} - name: test ABIN - run: make test && cd src/ && gcov *.o + run: make test && cd src/ && gcov ${GCOV_ARGS} *.o - name: Codecov upload uses: codecov/codecov-action@v3 with: @@ -360,7 +363,7 @@ jobs: FFLAGS: ${{ env.ABIN_FFLAGS }} LDLIBS: ${{ env.ABIN_LDLIBS }} - name: test ABIN - run: make test && cd src/ && gcov *.o + run: make test && cd src/ && gcov ${GCOV_ARGS} *.o - name: Codecov upload uses: codecov/codecov-action@v3 with: @@ -419,7 +422,7 @@ jobs: LDLIBS: ${{ env.ABIN_LDLIBS }} - name: Run Unit tests - run: make unittest && cd src/ && gcov *.o + run: make unittest && cd src/ && gcov ${GCOV_ARGS} *.o - name: Codecov upload unit tests uses: codecov/codecov-action@v3 @@ -428,7 +431,7 @@ jobs: flags: unittests - name: Run End-to-End tests - run: make e2etest && cd src/ && gcov *.o + run: make e2etest && cd src/ && gcov ${GCOV_ARGS} *.o - name: Codecov upload uses: codecov/codecov-action@v3 From bd1ccf1f4be283fbfb24690fa4d446e8790fe6db Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 19:26:07 +0100 Subject: [PATCH 23/61] Install g++-7 --- .github/workflows/gfortran.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index ba7b787a..c3255a3a 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -38,7 +38,7 @@ jobs: fetch-depth: 2 - name: Install GCC-7 - run: sudo apt install gcc-7 gfortran-7 + run: sudo apt install gcc-7 gfortran-7 g++-7 - name: Set GFortran version run: | From 0978931653390ab769a77c626352e821403b5462 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 19:39:09 +0100 Subject: [PATCH 24/61] Only install gcc-7 when needed --- .github/workflows/gfortran.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index c3255a3a..f82a5e07 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -38,6 +38,7 @@ jobs: fetch-depth: 2 - name: Install GCC-7 + if: matrix.gcc_v == 7 run: sudo apt install gcc-7 gfortran-7 g++-7 - name: Set GFortran version From 9348290c38060aaaa67c1a1eb54c32253c696e62 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 19:39:31 +0100 Subject: [PATCH 25/61] Try without codecov arguments --- .github/workflows/gfortran.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index f82a5e07..a5db4ac1 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -16,7 +16,7 @@ env: OPTIMIZED_FFLAGS: -O3 -fopenmp -fimplicit-none -Wall -Wno-integer-division # These are the defaults used in Codecov, see: # https://github.com/codecov/uploader/blob/main/src/helpers/gcov.ts - GCOV_ARGS: -pb + GCOV_ARGS: "" jobs: From effa4769bea29170dcc1de3d4c580ffaec7a0a3a Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 19:44:47 +0100 Subject: [PATCH 26/61] Back to 18 builds --- codecov.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/codecov.yml b/codecov.yml index 48f69e06..74a86345 100644 --- a/codecov.yml +++ b/codecov.yml @@ -5,7 +5,7 @@ codecov: # are completed, otherwise we'll temporarily receive # incomplete coverage reports. # Note that unit test coverage builds count towards the build count! - after_n_builds: 16 + after_n_builds: 18 wait_for_ci: yes coverage: From f1c63f6d74103192897fbde554f9f068c4629bfa Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 20:00:30 +0100 Subject: [PATCH 27/61] GCC-7 with mpich --- .github/workflows/gfortran.yml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index a5db4ac1..19739621 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -276,7 +276,7 @@ jobs: strategy: fail-fast: false matrix: - gcc_v: [9, 10] + gcc_v: [7, 10] mpich_v: ["3.4.3", "4.0.2"] env: # To speed-up MPICH build @@ -289,6 +289,11 @@ jobs: - uses: actions/checkout@v3 with: fetch-depth: 2 + + - name: Install GCC-7 + if: matrix.gcc_v == 7 + run: sudo apt install gcc-7 gfortran-7 g++-7 + - name: Set GFortran version run: | sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-${GCC_V} 100 \ From 35e190400153e10be6e5e45a5af8b2f8de9b03f7 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 20:29:24 +0100 Subject: [PATCH 28/61] -fprofile-abs-path --- .github/workflows/gfortran.yml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 19739621..482d7532 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -11,7 +11,7 @@ on: env: # FFLAGS for building ABIN, applicable for most jobs - ABIN_FFLAGS: -O0 -fopenmp --coverage -ffpe-trap=invalid,zero,overflow,denormal -fimplicit-none -Wall -Wno-integer-division -Wno-maybe-uninitialized + ABIN_FFLAGS: -O0 -fopenmp --coverage -fprofile-abs-path -finstrument-functions -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 # These are the defaults used in Codecov, see: @@ -67,7 +67,7 @@ jobs: LDLIBS: ${{ env.ABIN_LDLIBS }} - name: Run Unit tests - run: make unittest && cd src/ && gcov ${GCOV_ARGS} *.o + run: make unittest - name: Codecov upload unit tests uses: codecov/codecov-action@v3 @@ -76,13 +76,14 @@ jobs: flags: unittests - name: Run End-to-End tests - run: make e2etest && cd src/ && gcov ${GCOV_ARGS} *.o + run: make e2etest - name: Codecov upload uses: codecov/codecov-action@v3 with: name: ${{env.CODECOV_NAME}} fail_ci_if_error: true + gcov: true intel_build: name: Intel OneAPI build From 966023a7189378ebf1a369dc950fdf89d69ee1ec Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 20:45:05 +0100 Subject: [PATCH 29/61] gcc-7 doesn't have the -fprofiles-abs-path option --- .github/workflows/gfortran.yml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 482d7532..fbac9814 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -39,7 +39,9 @@ jobs: - name: Install GCC-7 if: matrix.gcc_v == 7 - run: sudo apt install gcc-7 gfortran-7 g++-7 + run: | + sudo apt install gcc-7 gfortran-7 g++-7 + echo "ABIN_FFLAGS=${ABIN_FFLAGS/-fprofile-abs-path/}" >> $GITHUB_ENV - name: Set GFortran version run: | @@ -293,7 +295,9 @@ jobs: - name: Install GCC-7 if: matrix.gcc_v == 7 - run: sudo apt install gcc-7 gfortran-7 g++-7 + run: | + sudo apt install gcc-7 gfortran-7 g++-7 + echo "ABIN_FFLAGS=${ABIN_FFLAGS/-fprofile-abs-path/}" >> $GITHUB_ENV - name: Set GFortran version run: | From b7ef49ab6a464f86ffc2c5f7f1086de31a017e2b Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 20:48:43 +0100 Subject: [PATCH 30/61] Update actions/cache --- .github/workflows/gfortran.yml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index fbac9814..420e7915 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -52,7 +52,7 @@ jobs: # pFUnit library is used to build and run unit tests - name: pFUnit build Cache id: pfunit-cache - uses: actions/cache@v2 + uses: actions/cache@v3 with: path: ~/pfunit/build/installed # To force a pFUnit rebuild (bust the cache), make a change to install_pfunit.sh @@ -145,7 +145,7 @@ jobs: - name: TCBP build cache id: tcpb-cache - uses: actions/cache@v2 + uses: actions/cache@v3 with: path: ~/tcpb-cpp/lib # To force a rebuild (bust the cache), make a change to install_tcpb.sh @@ -198,7 +198,7 @@ jobs: - name: pFUnit build Cache id: pfunit-cache - uses: actions/cache@v2 + uses: actions/cache@v3 with: path: ~/pfunit/build/installed key: ${{ runner.os }}-ubuntu22.04-pfunit-gfortran${{ env.GCC_V }}-${{ hashFiles('dev_scripts/install_pfunit.sh') }} @@ -238,7 +238,7 @@ jobs: - name: pFUnit build Cache id: pfunit-cache - uses: actions/cache@v2 + uses: actions/cache@v3 with: path: ~/pfunit/build/installed key: ${{ runner.os }}-ubuntu20.04-pfunit-gfortran-default-${{ hashFiles('dev_scripts/install_pfunit.sh') }} @@ -306,7 +306,7 @@ jobs: --slave /usr/bin/gcov gcov /usr/bin/gcov-${GCC_V} - name: MPICH build Cache id: mpich-cache - uses: actions/cache@v2 + uses: actions/cache@v3 with: path: ~/mpich/${{ env.MPICH_V }}/install key: ${{runner.os}}-ubuntu20.04-mpich${{ env.MPICH_V }}-gfortran${{ env.GCC_V }}-${{hashFiles('dev_scripts/install_mpich.sh')}} @@ -359,7 +359,7 @@ jobs: fetch-depth: 2 - name: OpenMPI build cache id: openmpi-cache - uses: actions/cache@v2 + uses: actions/cache@v3 with: path: ~/openmpi/${{ env.OPENMPI_V }}/install key: ${{runner.os}}-ubuntu20.04-openmpi${{ env.OPENMPI_V }}-gfortran-default-${{hashFiles('dev_scripts/install_openmpi.sh')}} @@ -403,7 +403,7 @@ jobs: fetch-depth: 2 - name: Plumed build cache id: plumed-cache - uses: actions/cache@v2 + uses: actions/cache@v3 with: path: ~/plumed/${{ env.PLUMED_V }}/install key: ${{runner.os}}-ubuntu20.04-plumed${{env.PLUMED_V}}-gcc-default-${{hashFiles('dev_scripts/install_plumed.sh')}} @@ -414,7 +414,7 @@ jobs: - name: pFUnit build Cache id: pfunit-cache - uses: actions/cache@v2 + uses: actions/cache@v3 with: path: ~/pfunit/build/installed key: ${{ runner.os }}-ubuntu20.04-pfunit-gfortran-default-${{ hashFiles('dev_scripts/install_pfunit.sh') }} From b6d445a70e8a87dbdf28ff05ce74e1c6c649fea5 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 20:58:20 +0100 Subject: [PATCH 31/61] fix unit test coverage --- .github/workflows/gfortran.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 420e7915..be817ca9 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -76,6 +76,7 @@ jobs: with: name: ${{env.CODECOV_NAME}} flags: unittests + gcov: true - name: Run End-to-End tests run: make e2etest From 477e67a1fc7a6c4ec9652930fe99c5a87a8ff9d1 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 21:15:49 +0100 Subject: [PATCH 32/61] Ignore utils --- codecov.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/codecov.yml b/codecov.yml index 74a86345..1fcd6373 100644 --- a/codecov.yml +++ b/codecov.yml @@ -37,3 +37,6 @@ comment: layout: "reach,diff,flags,tree" behavior: default require_changes: no + +ignore: + - "utils" From 01e35971ae2f2494f6132270423fe8fae946d5fa Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 21:20:59 +0100 Subject: [PATCH 33/61] fftw gcov from codecov --- .github/workflows/gfortran.yml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index be817ca9..f00aa6b9 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -219,14 +219,12 @@ jobs: - name: Run End-to-End tests run: make e2etest - # Here we just take the defaults everywhere, except turning on FFTW + # Here we just take the defaults everywhere, except installing libfftw via apt # To use FFTW with other Gfortran versions, we would need to build it. fftw_build: runs-on: ubuntu-20.04 name: FFTW build needs: basic_build - strategy: - fail-fast: false env: CODECOV_NAME: ${{format('{0}', github.job)}} steps: @@ -255,7 +253,7 @@ jobs: LDLIBS: ${{ env.ABIN_LDLIBS }} - name: Run Unit tests - run: make unittest && cd src/ && gcov ${GCOV_ARGS} *.o + run: make unittest - name: Codecov upload unit tests uses: codecov/codecov-action@v3 @@ -264,13 +262,14 @@ jobs: flags: unittests - name: Run End-to-End tests - run: make e2etest && cd src/ && gcov ${GCOV_ARGS} *.o + run: make e2etest - name: Codecov upload uses: codecov/codecov-action@v3 with: name: ${{env.CODECOV_NAME}} fail_ci_if_error: true + gcov: true mpich_build: name: MPICH build From 6d8a8c657568ed81ff65d335eec348a97bdee62c Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 21:23:29 +0100 Subject: [PATCH 34/61] plumed gcov --- .github/workflows/gfortran.yml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index f00aa6b9..034b736a 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -260,6 +260,7 @@ jobs: with: name: ${{env.CODECOV_NAME}} flags: unittests + gcov: true - name: Run End-to-End tests run: make e2etest @@ -433,19 +434,21 @@ jobs: LDLIBS: ${{ env.ABIN_LDLIBS }} - name: Run Unit tests - run: make unittest && cd src/ && gcov ${GCOV_ARGS} *.o + run: make unittest - name: Codecov upload unit tests uses: codecov/codecov-action@v3 with: name: ${{env.CODECOV_NAME}} flags: unittests + gcov: true - name: Run End-to-End tests - run: make e2etest && cd src/ && gcov ${GCOV_ARGS} *.o + run: make e2etest - name: Codecov upload uses: codecov/codecov-action@v3 with: name: ${{env.CODECOV_NAME}} fail_ci_if_error: true + gcov: true From e7cd6e9b1f505f7ae62ad19cb81d6fc4f5ceca49 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 21:26:59 +0100 Subject: [PATCH 35/61] gcov mpi --- .github/workflows/gfortran.yml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 034b736a..5e545128 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -163,13 +163,14 @@ jobs: LDLIBS: ${{ env.ABIN_LDLIBS }} - name: Run End-to-End tests - run: make e2etest && cd src/ && gcov ${GCOV_ARGS} *.o + run: make e2etest - name: Codecov upload uses: codecov/codecov-action@v3 with: name: tcpb fail_ci_if_error: true + gcov: true optimized_build: @@ -333,12 +334,13 @@ jobs: FFLAGS: ${{ env.ABIN_FFLAGS }} -g LDLIBS: ${{ env.ABIN_LDLIBS }} - name: test ABIN - run: make test && cd src/ && gcov ${GCOV_ARGS} *.o + run: make test - name: Codecov upload uses: codecov/codecov-action@v3 with: name: ${{env.CODECOV_NAME}} fail_ci_if_error: true + gcov: true openmpi_build: name: OpenMPI build @@ -375,12 +377,13 @@ jobs: FFLAGS: ${{ env.ABIN_FFLAGS }} LDLIBS: ${{ env.ABIN_LDLIBS }} - name: test ABIN - run: make test && cd src/ && gcov ${GCOV_ARGS} *.o + run: make test - name: Codecov upload uses: codecov/codecov-action@v3 with: name: ${{env.CODECOV_NAME}} fail_ci_if_error: true + gcov: true plumed_build: name: PLUMED build From 4761ee49bb08af376584e997c30431a619cc1920 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 21:30:13 +0100 Subject: [PATCH 36/61] Cleanup --- .github/workflows/gfortran.yml | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 5e545128..1e254d82 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -14,9 +14,6 @@ env: ABIN_FFLAGS: -O0 -fopenmp --coverage -fprofile-abs-path -finstrument-functions -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 - # These are the defaults used in Codecov, see: - # https://github.com/codecov/uploader/blob/main/src/helpers/gcov.ts - GCOV_ARGS: "" jobs: @@ -177,8 +174,6 @@ jobs: name: Optimized build # NOTE: We use a more recent Ubuntu version here # so we can test more recent GCC versions. - # NOTE: Because the cache key does not take into account OS version, - # we cannot test same GCC versions as in the basic build. runs-on: ubuntu-22.04 needs: basic_build strategy: @@ -323,12 +318,12 @@ jobs: # MPICH 4.0 also needs FCFLAGS set. # We also need to set it for ABIN compilation below. run: | - if [ $GCC_V -eq 10 ];then export FFLAGS="-fallow-argument-mismatch";export FCFLAGS="-fallow-argument-mismatch";fi && \ + if [ $GCC_V -ge 10 ];then export FFLAGS="-fallow-argument-mismatch";export FCFLAGS="-fallow-argument-mismatch";fi && \ ./dev_scripts/install_mpich.sh ${HOME}/mpich ${MPICH_V} - name: build ABIN run: | - if [ $GCC_V -eq 10 ];then export FFLAGS="-fallow-argument-mismatch $FFLAGS";fi && \ + if [ $GCC_V -ge 10 ];then export FFLAGS="-fallow-argument-mismatch $FFLAGS";fi && \ ./configure --mpi ${HOME}/mpich/${MPICH_V}/install && make env: FFLAGS: ${{ env.ABIN_FFLAGS }} -g From 9e4d2b040c5b52090988281678e885f95847c66d Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 21:45:55 +0100 Subject: [PATCH 37/61] Try without -finstrument-functions --- .github/workflows/gfortran.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 1e254d82..8e7e8b67 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -11,7 +11,7 @@ on: env: # FFLAGS for building ABIN, applicable for most jobs - ABIN_FFLAGS: -O0 -fopenmp --coverage -fprofile-abs-path -finstrument-functions -ffpe-trap=invalid,zero,overflow,denormal -fimplicit-none -Wall -Wno-integer-division -Wno-maybe-uninitialized + 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 From 26f1805baf4682261a51b0db6b7b9081a1da20e9 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 21:54:24 +0100 Subject: [PATCH 38/61] try -Og for fftw build --- .github/workflows/gfortran.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 8e7e8b67..00a12436 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -245,7 +245,7 @@ jobs: - name: Build ABIN run: ./configure --pfunit ${HOME}/pfunit/build/installed/ --fftw && make env: - FFLAGS: ${{ env.ABIN_FFLAGS }} + FFLAGS: ${{ env.ABIN_FFLAGS }} -Og LDLIBS: ${{ env.ABIN_LDLIBS }} - name: Run Unit tests From e564cc8aa50be713085ddddc8b0b5dec813e4aff Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 22:22:35 +0100 Subject: [PATCH 39/61] Try ubuntu 22.04 for the fftw build --- .github/workflows/gfortran.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 00a12436..49257ed2 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -218,7 +218,7 @@ jobs: # Here we just take the defaults everywhere, except installing libfftw via apt # To use FFTW with other Gfortran versions, we would need to build it. fftw_build: - runs-on: ubuntu-20.04 + runs-on: ubuntu-22.04 name: FFTW build needs: basic_build env: @@ -236,7 +236,7 @@ jobs: uses: actions/cache@v3 with: path: ~/pfunit/build/installed - key: ${{ runner.os }}-ubuntu20.04-pfunit-gfortran-default-${{ hashFiles('dev_scripts/install_pfunit.sh') }} + key: ${{ runner.os }}-ubuntu22.04-pfunit-gfortran-default-${{ hashFiles('dev_scripts/install_pfunit.sh') }} - name: Download and build pFUnit if: steps.pfunit-cache.outputs.cache-hit != 'true' @@ -245,7 +245,7 @@ jobs: - name: Build ABIN run: ./configure --pfunit ${HOME}/pfunit/build/installed/ --fftw && make env: - FFLAGS: ${{ env.ABIN_FFLAGS }} -Og + FFLAGS: ${{ env.ABIN_FFLAGS }} LDLIBS: ${{ env.ABIN_LDLIBS }} - name: Run Unit tests From 7e9ee7070844db1e60394b55dbb25bfeaceb4643 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 22:46:09 +0100 Subject: [PATCH 40/61] try enabling method and macro branch detection --- codecov.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/codecov.yml b/codecov.yml index 1fcd6373..3be6773f 100644 --- a/codecov.yml +++ b/codecov.yml @@ -30,8 +30,8 @@ parsers: branch_detection: conditional: yes loop: yes - method: no - macro: no + method: yes + macro: yes comment: layout: "reach,diff,flags,tree" From a50d4f3809c3ee54f75a5c3191ae7732cd3870dd Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 12 Apr 2023 23:00:47 +0100 Subject: [PATCH 41/61] Revert "try enabling method and macro branch detection" This reverts commit 7e9ee7070844db1e60394b55dbb25bfeaceb4643. --- codecov.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/codecov.yml b/codecov.yml index 3be6773f..1fcd6373 100644 --- a/codecov.yml +++ b/codecov.yml @@ -30,8 +30,8 @@ parsers: branch_detection: conditional: yes loop: yes - method: yes - macro: yes + method: no + macro: no comment: layout: "reach,diff,flags,tree" From 764728a765f178f71649b86bb2700e83f48b06bb Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sat, 15 Apr 2023 16:08:33 +0100 Subject: [PATCH 42/61] Add -fcheck=all compilation flag --- .github/workflows/gfortran.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 49257ed2..60801ca6 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -11,7 +11,7 @@ on: env: # FFLAGS for building ABIN, applicable for most jobs - ABIN_FFLAGS: -O0 -fopenmp --coverage -fprofile-abs-path -ffpe-trap=invalid,zero,overflow,denormal -fimplicit-none -Wall -Wno-integer-division -Wno-maybe-uninitialized + ABIN_FFLAGS: -O0 -fopenmp --coverage -fprofile-abs-path -fcheck=all -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 From e72ae20cb2f9c47058cf6e31ce850651b2579d42 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sat, 15 Apr 2023 16:12:53 +0100 Subject: [PATCH 43/61] -fno-inline --- .github/workflows/gfortran.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 60801ca6..a1b926f5 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -11,7 +11,7 @@ on: env: # FFLAGS for building ABIN, applicable for most jobs - ABIN_FFLAGS: -O0 -fopenmp --coverage -fprofile-abs-path -fcheck=all -ffpe-trap=invalid,zero,overflow,denormal -fimplicit-none -Wall -Wno-integer-division -Wno-maybe-uninitialized + ABIN_FFLAGS: -O0 -fopenmp --coverage -fprofile-abs-path -fno-inline -fcheck=all -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 From 72a7665694148f526052d0f066eb267b2bdac491 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sat, 15 Apr 2023 16:57:25 +0100 Subject: [PATCH 44/61] Fix out-of-bounds array access in nhc init --- src/nosehoover.F90 | 30 ++++++++++++++++-------------- tests/INIT/test.sh | 2 +- 2 files changed, 17 insertions(+), 15 deletions(-) diff --git a/src/nosehoover.F90 b/src/nosehoover.F90 index 340720c1..77b83160 100644 --- a/src/nosehoover.F90 +++ b/src/nosehoover.F90 @@ -108,6 +108,13 @@ subroutine check_nhc_parameters() error = .false. + call int_nonnegative(inose, 'inose') + call int_positive(nchain, 'nchain') + call int_positive(nrespnose, 'nrespnose') + call int_positive(nmolt, 'nmolt') + call int_switch(imasst, 'imasst') + call real_nonnegative(temp, 'temp') + if (nchain > maxchain) then write (stderr, '(A)') 'Maximum number of Nose-Hoover chains exceeded' error = .true. @@ -131,9 +138,17 @@ subroutine check_nhc_parameters() error = .true. end if + if (temp * AUTOK < 1 .and. inose > 0) then + write (stderr, '(A)') 'Temperature below 1 Kelvin. Are you sure?' + write (stderr, '(A)') chknow + if (iknow /= 1) error = .true. + end if + if (nmolt > natom) then write (stdout, '(A)') 'nmolt > natom, which is not possible. Consult the manual.' - error = .true. + ! We need to exit early here, otherwise we risk out-of-bounds arrays access below + call fatal_error(__FILE__, __LINE__, & + & 'Invalid NHC thermostat parameter(s)') end if if (imasst == 0) then @@ -157,19 +172,6 @@ subroutine check_nhc_parameters() end if end if - if (temp * AUTOK < 1 .and. inose > 0) then - write (stderr, '(A)') 'Temperature below 1 Kelvin. Are you sure?' - write (stderr, '(A)') chknow - if (iknow /= 1) error = .true. - end if - - call int_nonnegative(inose, 'inose') - call int_positive(nchain, 'nchain') - call int_positive(nrespnose, 'nrespnose') - call int_positive(nmolt, 'nmolt') - call int_switch(imasst, 'imasst') - call real_nonnegative(temp, 'temp') - if (error) then call fatal_error(__FILE__, __LINE__, & & 'Invalid NHC thermostat parameter(s)') diff --git a/tests/INIT/test.sh b/tests/INIT/test.sh index ff9da6cb..22169c1b 100755 --- a/tests/INIT/test.sh +++ b/tests/INIT/test.sh @@ -2,7 +2,7 @@ set -euo pipefail -rm -f ERROR abin.out movie.xyz restart.xyz *dat +rm -f ERROR ABIN_ERROR? abin.out movie.xyz restart.xyz *dat if [[ $1 = "clean" ]];then exit 0 fi From 3d01eca59fd165c76ac02f58cd7ac7967aaa293b Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sat, 15 Apr 2023 17:14:14 +0100 Subject: [PATCH 45/61] no-early-inlining --- .github/workflows/gfortran.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index a1b926f5..e55614e9 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -11,7 +11,7 @@ on: env: # FFLAGS for building ABIN, applicable for most jobs - ABIN_FFLAGS: -O0 -fopenmp --coverage -fprofile-abs-path -fno-inline -fcheck=all -ffpe-trap=invalid,zero,overflow,denormal -fimplicit-none -Wall -Wno-integer-division -Wno-maybe-uninitialized + ABIN_FFLAGS: -O0 -fopenmp --coverage -fprofile-abs-path -fno-early-inlining -fcheck=all -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 From f14fcfc9a92a42ca76b2ecdb6368e2f8bcc82047 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sat, 15 Apr 2023 17:26:50 +0100 Subject: [PATCH 46/61] revert --- .github/workflows/gfortran.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index e55614e9..49257ed2 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -11,7 +11,7 @@ on: env: # FFLAGS for building ABIN, applicable for most jobs - ABIN_FFLAGS: -O0 -fopenmp --coverage -fprofile-abs-path -fno-early-inlining -fcheck=all -ffpe-trap=invalid,zero,overflow,denormal -fimplicit-none -Wall -Wno-integer-division -Wno-maybe-uninitialized + 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 From c2569a8481d5c8757023191c6057b55bca3071a0 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sat, 15 Apr 2023 17:39:43 +0100 Subject: [PATCH 47/61] fcheck not all --- .github/workflows/gfortran.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 49257ed2..5fd48a19 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -245,7 +245,7 @@ jobs: - name: Build ABIN run: ./configure --pfunit ${HOME}/pfunit/build/installed/ --fftw && make env: - FFLAGS: ${{ env.ABIN_FFLAGS }} + FFLAGS: ${{ env.ABIN_FFLAGS }} -fcheck=all,no-mem,no-pointer LDLIBS: ${{ env.ABIN_LDLIBS }} - name: Run Unit tests From 29fc214a7a435fad988a7aa827d995fa11767fc0 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sat, 15 Apr 2023 17:53:20 +0100 Subject: [PATCH 48/61] -g --- .github/workflows/gfortran.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 5fd48a19..75f4d21c 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -11,7 +11,7 @@ on: env: # FFLAGS for building ABIN, applicable for most jobs - ABIN_FFLAGS: -O0 -fopenmp --coverage -fprofile-abs-path -ffpe-trap=invalid,zero,overflow,denormal -fimplicit-none -Wall -Wno-integer-division -Wno-maybe-uninitialized + ABIN_FFLAGS: -g -Og -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 @@ -245,7 +245,7 @@ jobs: - name: Build ABIN run: ./configure --pfunit ${HOME}/pfunit/build/installed/ --fftw && make env: - FFLAGS: ${{ env.ABIN_FFLAGS }} -fcheck=all,no-mem,no-pointer + FFLAGS: ${{ env.ABIN_FFLAGS }} LDLIBS: ${{ env.ABIN_LDLIBS }} - name: Run Unit tests From 2545f39d8341c4ccec294d7e4bfceaa63d108fa2 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sat, 15 Apr 2023 18:20:06 +0100 Subject: [PATCH 49/61] fcheck and fsanitize conditionally --- .github/workflows/gfortran.yml | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 75f4d21c..b26f2575 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -11,7 +11,7 @@ on: env: # FFLAGS for building ABIN, applicable for most jobs - ABIN_FFLAGS: -g -Og -fopenmp --coverage -fprofile-abs-path -ffpe-trap=invalid,zero,overflow,denormal -fimplicit-none -Wall -Wno-integer-division -Wno-maybe-uninitialized + ABIN_FFLAGS: -O0 -fopenmp --coverage -fprofile-abs-path -ffpe-trap=invalid,zero,overflow,denormal -fimplicit-none -Wall -Wno-integer-division -Wno-maybe-uninitialized ABIN_LDLIBS: --coverage OPTIMIZED_FFLAGS: -O3 -fopenmp -fimplicit-none -Wall -Wno-integer-division @@ -40,6 +40,13 @@ jobs: sudo apt install gcc-7 gfortran-7 g++-7 echo "ABIN_FFLAGS=${ABIN_FFLAGS/-fprofile-abs-path/}" >> $GITHUB_ENV + - name: Enable runtime checks + # It looks like this messes up the code coverage, so enabling only some builds + if: matrix.gcc_v != 7 + run: | + echo "ABIN_FFLAGS=${ABIN_FFLAGS} -fcheck=all -fsanitize=address,undefined,leak" >> $GITHUB_ENV + echo "ABIN_LDFLAGS=${ABIN_LDFLAGS -fsanitize=address,undefined,leak" >> $GITHUB_ENV + - name: Set GFortran version run: | sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-${GCC_V} 100 \ From 48c2a160c5ff9206155a051de9f3e06e9ec20636 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sat, 15 Apr 2023 18:21:59 +0100 Subject: [PATCH 50/61] fix --- .github/workflows/gfortran.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index b26f2575..144dbb5c 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -45,7 +45,7 @@ jobs: if: matrix.gcc_v != 7 run: | echo "ABIN_FFLAGS=${ABIN_FFLAGS} -fcheck=all -fsanitize=address,undefined,leak" >> $GITHUB_ENV - echo "ABIN_LDFLAGS=${ABIN_LDFLAGS -fsanitize=address,undefined,leak" >> $GITHUB_ENV + echo "ABIN_LDFLAGS=${ABIN_LDFLAGS} -fsanitize=address,undefined,leak" >> $GITHUB_ENV - name: Set GFortran version run: | From 2abff53a3dd253c1c078d9fc175307cb7397afbe Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sat, 15 Apr 2023 18:23:49 +0100 Subject: [PATCH 51/61] more fix --- .github/workflows/gfortran.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 144dbb5c..5d3f40c9 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -45,7 +45,7 @@ jobs: if: matrix.gcc_v != 7 run: | echo "ABIN_FFLAGS=${ABIN_FFLAGS} -fcheck=all -fsanitize=address,undefined,leak" >> $GITHUB_ENV - echo "ABIN_LDFLAGS=${ABIN_LDFLAGS} -fsanitize=address,undefined,leak" >> $GITHUB_ENV + echo "ABIN_LDLIBS=${ABIN_LDLIBS} -fsanitize=address,undefined,leak" >> $GITHUB_ENV - name: Set GFortran version run: | From 81e074dce17fdf75885527aaae2f91ad94adeb42 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sat, 15 Apr 2023 18:31:29 +0100 Subject: [PATCH 52/61] always run e2etest even if unit tests fail --- .github/workflows/gfortran.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/gfortran.yml b/.github/workflows/gfortran.yml index 5d3f40c9..f9e122a1 100644 --- a/.github/workflows/gfortran.yml +++ b/.github/workflows/gfortran.yml @@ -83,6 +83,7 @@ jobs: gcov: true - name: Run End-to-End tests + if: always() run: make e2etest - name: Codecov upload From f12f5bcf01221b47ec8dd3bf44c6f279447d2033 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sat, 15 Apr 2023 18:36:29 +0100 Subject: [PATCH 53/61] Do not run MM unit tests --- unit_tests/Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/unit_tests/Makefile b/unit_tests/Makefile index 7c18a0dc..8d12c007 100755 --- a/unit_tests/Makefile +++ b/unit_tests/Makefile @@ -129,7 +129,7 @@ test : clean_plumed_output clean_terapi_output clean_gle_output ./gle ./nhc ./pot - ./mm + #./mm ./spline ./io ./interface From cf292daddc70aca4d59f34f4bba2e61f2fa12f6d Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sat, 15 Apr 2023 18:40:12 +0100 Subject: [PATCH 54/61] Do not run spline unit tests --- unit_tests/Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/unit_tests/Makefile b/unit_tests/Makefile index 8d12c007..3b81d2cf 100755 --- a/unit_tests/Makefile +++ b/unit_tests/Makefile @@ -130,7 +130,7 @@ test : clean_plumed_output clean_terapi_output clean_gle_output ./nhc ./pot #./mm - ./spline + #./spline ./io ./interface From eaa344fead5a6dc9e5339cd21ccc6382b4efe348 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sat, 15 Apr 2023 18:49:21 +0100 Subject: [PATCH 55/61] Fix MM leak? --- src/force_mm.F90 | 2 ++ unit_tests/Makefile | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/src/force_mm.F90 b/src/force_mm.F90 index 37c03549..79298d59 100644 --- a/src/force_mm.F90 +++ b/src/force_mm.F90 @@ -53,6 +53,7 @@ subroutine initialize_mm(natom, names, atom_types, charges, LJ_rmin, LJ_eps) call flush (stdout) call flush (stderr) write (stdout, '(A)') '' + deallocate (normalized_atom_types) end subroutine initialize_mm subroutine finalize_mm() @@ -90,6 +91,7 @@ function normalize_atom_types(atom_types) result(attypes) attypes(itype) = normalize_atom_name(atom_types(i)) itype = itype + 1 end do + deallocate (attypes) end function normalize_atom_types ! Here we create the mapping from atom index diff --git a/unit_tests/Makefile b/unit_tests/Makefile index 3b81d2cf..215d63a9 100755 --- a/unit_tests/Makefile +++ b/unit_tests/Makefile @@ -129,7 +129,7 @@ test : clean_plumed_output clean_terapi_output clean_gle_output ./gle ./nhc ./pot - #./mm + ./mm #./spline ./io ./interface From 56aa52e86e84afc4af597b5b4ce80dd78ce9b0a2 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sat, 15 Apr 2023 19:02:54 +0100 Subject: [PATCH 56/61] Deallocate fix --- src/force_mm.F90 | 1 - 1 file changed, 1 deletion(-) diff --git a/src/force_mm.F90 b/src/force_mm.F90 index 79298d59..3776d636 100644 --- a/src/force_mm.F90 +++ b/src/force_mm.F90 @@ -91,7 +91,6 @@ function normalize_atom_types(atom_types) result(attypes) attypes(itype) = normalize_atom_name(atom_types(i)) itype = itype + 1 end do - deallocate (attypes) end function normalize_atom_types ! Here we create the mapping from atom index From 9c1d760cb4730a5e26dc6167114d6a88b6fcf2f2 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sat, 15 Apr 2023 19:09:44 +0100 Subject: [PATCH 57/61] Disable most tests --- unit_tests/test_mm.pf | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/unit_tests/test_mm.pf b/unit_tests/test_mm.pf index 8d3050a5..c958285c 100644 --- a/unit_tests/test_mm.pf +++ b/unit_tests/test_mm.pf @@ -61,6 +61,7 @@ contains end subroutine @test + @disable subroutine test_like_charges() types = (/'Kr', 'Xe'/) names = types @@ -97,6 +98,7 @@ contains @assertLessThan(fz(1, 1), 0.0D0, 'fz repel') end subroutine + @disable subroutine test_opposite_charges() types = (/'Kr', 'Xe'/) names = types @@ -124,6 +126,7 @@ contains end subroutine @test + @disable subroutine test_LJ_minimum() real(DP), dimension(NATOM, NWALK) :: fzero = 0.0D0 real(DP) :: E_min @@ -152,6 +155,7 @@ contains end subroutine @test + @disable subroutine test_bead_scaling() integer, parameter :: NTYPES = 2 real(DP), dimension(NATOM, NWALK) :: fx1, fy1, fz1 From 39dc95082683d3a5538e697a245531c765964a15 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Sat, 15 Apr 2023 19:15:45 +0100 Subject: [PATCH 58/61] Remove disabled macro --- unit_tests/Makefile | 2 +- unit_tests/test_mm.pf | 8 -------- unit_tests/test_spline.pf | 4 ++-- 3 files changed, 3 insertions(+), 11 deletions(-) diff --git a/unit_tests/Makefile b/unit_tests/Makefile index 215d63a9..7c18a0dc 100755 --- a/unit_tests/Makefile +++ b/unit_tests/Makefile @@ -130,7 +130,7 @@ test : clean_plumed_output clean_terapi_output clean_gle_output ./nhc ./pot ./mm - #./spline + ./spline ./io ./interface diff --git a/unit_tests/test_mm.pf b/unit_tests/test_mm.pf index c958285c..dbe94093 100644 --- a/unit_tests/test_mm.pf +++ b/unit_tests/test_mm.pf @@ -61,7 +61,6 @@ contains end subroutine @test - @disable subroutine test_like_charges() types = (/'Kr', 'Xe'/) names = types @@ -98,7 +97,6 @@ contains @assertLessThan(fz(1, 1), 0.0D0, 'fz repel') end subroutine - @disable subroutine test_opposite_charges() types = (/'Kr', 'Xe'/) names = types @@ -126,7 +124,6 @@ contains end subroutine @test - @disable subroutine test_LJ_minimum() real(DP), dimension(NATOM, NWALK) :: fzero = 0.0D0 real(DP) :: E_min @@ -155,7 +152,6 @@ contains end subroutine @test - @disable subroutine test_bead_scaling() integer, parameter :: NTYPES = 2 real(DP), dimension(NATOM, NWALK) :: fx1, fy1, fz1 @@ -208,8 +204,6 @@ contains end subroutine ! Helper function if you want to check the potential - @test - @disable subroutine print_lj_potential() integer, parameter :: NATOM = 2, NWALK = 1 real(DP) :: r0, rmax, r, dr @@ -248,8 +242,6 @@ contains close (u) end subroutine - @test - @disable subroutine print_coulomb_potential() integer, parameter :: NATOM = 2, NWALK = 1 real(DP) :: r0, rmax, r, dr diff --git a/unit_tests/test_spline.pf b/unit_tests/test_spline.pf index a8163377..70fe7a33 100644 --- a/unit_tests/test_spline.pf +++ b/unit_tests/test_spline.pf @@ -117,8 +117,8 @@ contains ! TODO: This needs to throw before the FP exception ! For some reason, missing y-value does not trip the read statement. :-( - @test - @disable + !@test + !@disable subroutine test_validate_grid_values() integer :: u From c50735665df33a3da5584dc1f9939980c385bbef Mon Sep 17 00:00:00 2001 From: Jiri Janos Date: Mon, 17 Apr 2023 17:54:22 +0200 Subject: [PATCH 59/61] Addressing comments of DH from previous pull request The only significant change is a new condition for discontinuities. --- src/landau_zener.F90 | 21 +++++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) diff --git a/src/landau_zener.F90 b/src/landau_zener.F90 index 6f517985..648081e4 100644 --- a/src/landau_zener.F90 +++ b/src/landau_zener.F90 @@ -3,6 +3,7 @@ ! Nonadiabatic nuclear dynamics of atomic collisions based on branching classical trajectories ! Andrey K. Belyaev and Oleg V. Lebedev ! Implemented by: J. Suchan, (J. Chalabala) +! Modified by J. Janos (2023) ! No S/T TeraChem functionality YET ! No energy drift check @@ -19,7 +20,7 @@ module mod_lz implicit none private public :: lz_init, lz_hop, lz_rewind, lz_restin, lz_restout, lz_finalize !Routines - public :: initstate_lz, nstate_lz, nsinglet_lz, ntriplet_lz, deltaE_lz, energydifthr_lz !User defined variables + public :: initstate_lz, nstate_lz, nsinglet_lz, ntriplet_lz, deltaE_lz, energydifthr_lz !User defined variables, [deltaE_lz] = eV public :: en_array_lz, tocalc_lz, istate_lz !Routine variables !Caveat: Every time we call force_clas en_array_lz is updated @@ -203,10 +204,22 @@ subroutine lz_hop(x, y, z, vx, vy, vz, fxc, fyc, fzc, amt, dt, eclas, chpot) ! only for significant probabilities, for tiny probabilities this does not make sense ! e.g. for parallel states (the whole LZ does not make sense for this case) if (prob(ist1) > 0.01) then + ! Calculating backward second derivative formula. We are not using the newest energy + ! but the previous three. Discontinuity would not affect this formula. second_der_back = ((en_diff(2) - 2 * en_diff(3) + en_diff(4)) / dt**2) + ! We have central and backward second derivative formulas and compare them. + ! If the change is too large, we either almost hit the CI or we have discontinuity. der_check = abs((second_der - second_der_back) / second_der) - if (der_check > 0.3) then - write (*,*) "WARNING, possible discontinuity in PES! Check PES.dat!" + ! If they differ by more then 130%, we have aa unphysical change of curvature --> certain discontinuity. + if (der_check > 1.3) then + write (stdout,*) "ERROR: Change of curvature --> discontinuity in PES!" + write (stdout,*) "Probability set to 0!" + prob(ist1) = 0.0d + ! 30% threshold was set empirically and should capture most discontinuities + ! yet it can also be a conical intersection. Thus, we just issue an warning + ! and let the user to evaluate on his own. + else if (der_check > 0.3) then + write (stdout,*) "WARNING: Possible discontinuity in PES! Check PES.dat!" end if end if @@ -215,7 +228,7 @@ subroutine lz_hop(x, y, z, vx, vy, vz, fxc, fyc, fzc, amt, dt, eclas, chpot) ! LZ warning if (sum(prob) > 1) then - write (*,*) "* WARNING, sum of hopping probabilities > 1. Breakdown of LZ assumptions" + write (stdout, *) "WARNING: Sum of hopping probabilities > 1. Breakdown of LZ assumptions" end if !Hop? From 01a788944e17afc6f5242838238fce12f4b55e5b Mon Sep 17 00:00:00 2001 From: Jiri Janos Date: Tue, 18 Apr 2023 14:36:23 +0200 Subject: [PATCH 60/61] Correcting typo and modified test reference for LZ_SS --- src/landau_zener.F90 | 2 +- tests/LZ_SS/pop.dat.ref | 16 ++++++++-------- tests/LZ_SS/restart.xyz.ref | 28 ++++++++++++++-------------- 3 files changed, 23 insertions(+), 23 deletions(-) diff --git a/src/landau_zener.F90 b/src/landau_zener.F90 index 648081e4..20ba4a59 100644 --- a/src/landau_zener.F90 +++ b/src/landau_zener.F90 @@ -214,7 +214,7 @@ subroutine lz_hop(x, y, z, vx, vy, vz, fxc, fyc, fzc, amt, dt, eclas, chpot) if (der_check > 1.3) then write (stdout,*) "ERROR: Change of curvature --> discontinuity in PES!" write (stdout,*) "Probability set to 0!" - prob(ist1) = 0.0d + prob(ist1) = 0.0D0 ! 30% threshold was set empirically and should capture most discontinuities ! yet it can also be a conical intersection. Thus, we just issue an warning ! and let the user to evaluate on his own. diff --git a/tests/LZ_SS/pop.dat.ref b/tests/LZ_SS/pop.dat.ref index 2e8c5ceb..a60e522f 100644 --- a/tests/LZ_SS/pop.dat.ref +++ b/tests/LZ_SS/pop.dat.ref @@ -1,11 +1,11 @@ # Time[fs] CurrentState Populations Sum-of-Populations 0.24 2 0.00000 1.00000 0.00000 1.0000000 0.48 2 0.00000 1.00000 0.00000 1.0000000 - 0.73 1 1.00000 0.00000 0.00000 1.0000000 - 0.97 1 1.00000 0.00000 0.00000 1.0000000 - 1.21 1 1.00000 0.00000 0.00000 1.0000000 - 1.45 1 1.00000 0.00000 0.00000 1.0000000 - 1.69 2 0.00000 1.00000 0.00000 1.0000000 - 1.94 2 0.00000 1.00000 0.00000 1.0000000 - 2.18 2 0.00000 1.00000 0.00000 1.0000000 - 2.42 2 0.00000 1.00000 0.00000 1.0000000 + 0.73 2 0.00000 1.00000 0.00000 1.0000000 + 0.97 2 0.00000 1.00000 0.00000 1.0000000 + 1.21 2 0.00000 1.00000 0.00000 1.0000000 + 1.45 2 0.00000 1.00000 0.00000 1.0000000 + 1.69 1 1.00000 0.00000 0.00000 1.0000000 + 1.94 1 1.00000 0.00000 0.00000 1.0000000 + 2.18 1 1.00000 0.00000 0.00000 1.0000000 + 2.42 1 1.00000 0.00000 0.00000 1.0000000 diff --git a/tests/LZ_SS/restart.xyz.ref b/tests/LZ_SS/restart.xyz.ref index e787a7ed..49204907 100644 --- a/tests/LZ_SS/restart.xyz.ref +++ b/tests/LZ_SS/restart.xyz.ref @@ -1,20 +1,20 @@ 10 1.0000000000000000E+002 Cartesian Coordinates [au] - -1.9364324259617078E+000 -2.6605292764925466E+000 -1.0224417442984338E-001 - 8.6997754122248017E-001 1.8901712905272237E+000 1.8207823291854579E+000 - -7.6329981664742508E-001 -3.4963405866520754E+000 -1.2168279443797034E+000 - -3.0492007055536154E+000 -1.2311514676572006E+000 9.2861134409524548E-001 - 2.1011884380249390E+000 6.1690339979383801E-001 2.3652616421347288E+000 - 2.6883938075810634E+000 2.6243408598405322E+000 5.2608370645489433E-001 + -1.9365183200983036E+000 -2.6602216188713359E+000 -1.0174174012800434E-001 + 8.6986078957715707E-001 1.8900955889241788E+000 1.8206592318094852E+000 + -7.6328954567703133E-001 -3.4960846412813678E+000 -1.2188110161818635E+000 + -3.0465628206263489E+000 -1.2330430649713027E+000 9.2537836196433088E-001 + 2.1012084586483355E+000 6.1663430787465434E-001 2.3663987245031106E+000 + 2.6883714790490081E+000 2.6236315923904052E+000 5.2588637497256596E-001 Cartesian Velocities [au] - -6.2541331318772945E-004 -1.7186982965908355E-003 -3.0636402554938660E-004 - 2.7528787990875413E-004 7.9328082231737386E-004 7.1632940330620780E-004 - 1.8493150786253330E-004 3.3111172738813826E-003 5.4067050942694283E-004 - -1.0103552429958959E-003 4.3434957130716679E-003 -1.8806176502816256E-003 - 5.8628716364069898E-004 2.2733862602508252E-004 -3.8094988094623606E-003 - 3.8660035998388060E-003 1.5741999368462552E-003 -1.1540140006298522E-003 + -6.2755594627401815E-004 -1.7173102504899852E-003 -3.0045825709899094E-004 + 2.7436967418411311E-004 7.9355452819480324E-004 7.1577356895686660E-004 + 1.8595121756919664E-004 3.3186075015489520E-003 5.1619868205874547E-004 + -9.7822393035781430E-004 4.3254426983749678E-003 -1.9244771504258028E-003 + 5.8738078497950531E-004 2.2387167111950917E-004 -3.8001837004373127E-003 + 3.8700491085375040E-003 1.5678868010034360E-003 -1.1576452159969396E-003 Energy difference history for LZ - 2 + 1 -9.4089625847768389E+001 -9.4089734388134346E+001 -9.4089721321419489E+001 -9.4089611644167093E+001 -9.4084269652748361E+001 -9.4085985079607525E+001 -9.4087433859349289E+001 @@ -22,7 +22,7 @@ -9.3999270951262247E+001 -9.3999358990659246E+001 -9.3999541872297826E+001 -9.3999788225478142E+001 Cumulative averages of various estimators - 1.0362047031511409E-001 + 1.0331026844288205E-001 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 PRNG STATE (OPTIONAL) From a91c6bc356355d88980ba4f194945659b1718d07 Mon Sep 17 00:00:00 2001 From: Jiri Janos Date: Fri, 14 Jul 2023 14:52:04 +0200 Subject: [PATCH 61/61] Modifying TERAPI-LZ test Modification of TERAPI-LZ test to be compatible with the new modifications of the LZ algorithm. The problem was just three steps. Thus, the previous second derivative used in the discontinuity check was still set to 0 which caused the code to think there is a discontinuity. One more step was artificially added so that it has also the previous second derivative. --- tests/TERAPI-LZ/PES.dat.ref | 7 ++++--- tests/TERAPI-LZ/allenergies | 3 ++- tests/TERAPI-LZ/allforces | 8 ++++++++ tests/TERAPI-LZ/forces.xyz.ref | 12 +++++++++-- tests/TERAPI-LZ/input.in | 2 +- tests/TERAPI-LZ/movie.xyz.ref | 20 +++++++++++++------ tests/TERAPI-LZ/pop.dat.ref | 3 ++- tests/TERAPI-LZ/velocities.xyz.ref | 32 +++++++++++++++++++----------- 8 files changed, 61 insertions(+), 26 deletions(-) diff --git a/tests/TERAPI-LZ/PES.dat.ref b/tests/TERAPI-LZ/PES.dat.ref index b26139e1..4e907582 100644 --- a/tests/TERAPI-LZ/PES.dat.ref +++ b/tests/TERAPI-LZ/PES.dat.ref @@ -1,4 +1,5 @@ # Time[fs] Potential energies (singlets, triplets) - 0.24 -0.9437392408E+02 -0.9403262935E+02 -0.9402002913E+02 - 0.48 -0.9436548900E+02 -0.9402359689E+02 -0.9401931954E+02 - 0.73 -0.9435659011E+02 -0.9401940034E+02 -0.9401348411E+02 + 0.24 -0.9437392408E+02 -0.9404732907E+02 -0.9402002913E+02 + 0.48 -0.9437392408E+02 -0.9403262935E+02 -0.9402002913E+02 + 0.73 -0.9436548900E+02 -0.9402359689E+02 -0.9401931954E+02 + 0.97 -0.9435659011E+02 -0.9401940034E+02 -0.9401348411E+02 diff --git a/tests/TERAPI-LZ/allenergies b/tests/TERAPI-LZ/allenergies index cef72707..360fd21e 100644 --- a/tests/TERAPI-LZ/allenergies +++ b/tests/TERAPI-LZ/allenergies @@ -1,4 +1,5 @@ --0.9437392408E+02 -0.9403262935E+02 -0.9402002913E+02 +-0.9437392408E+02 -0.9404732907E+02 -0.9402002913E+02 +-0.9437392408E+02 -0.9404732907E+02 -0.9402002913E+02 -0.9437392408E+02 -0.9403262935E+02 -0.9402002913E+02 -0.9436548900E+02 -0.9402359689E+02 -0.9401931954E+02 -0.9435659011E+02 -0.9401940034E+02 -0.9401348411E+02 diff --git a/tests/TERAPI-LZ/allforces b/tests/TERAPI-LZ/allforces index 2e126b0b..12979f8f 100644 --- a/tests/TERAPI-LZ/allforces +++ b/tests/TERAPI-LZ/allforces @@ -16,6 +16,14 @@ H -0.2782826117E-01 -0.1670370136E-02 0.3235792249E-01 H -0.1192180436E+00 0.1363320697E-01 -0.7406869050E-01 6 comment +C 0.1394112435E+00 -0.1118998196E-01 -0.1461160381E+00 +N 0.3739084695E-01 -0.2565077705E-02 0.1496980461E+00 +H -0.2347502477E-01 -0.5726225634E-02 0.4997758573E-02 +H -0.6280761008E-02 0.7518448370E-02 0.3313100155E-01 +H -0.2782826117E-01 -0.1670370136E-02 0.3235792249E-01 +H -0.1192180436E+00 0.1363320697E-01 -0.7406869050E-01 + 6 +comment C 0.1453320682E+00 -0.1833857157E-01 -0.7561297419E-01 N 0.6556333519E-01 0.2833881964E-02 0.8552960343E-01 H -0.1427369250E-01 -0.1469574481E-01 -0.3602639052E-02 diff --git a/tests/TERAPI-LZ/forces.xyz.ref b/tests/TERAPI-LZ/forces.xyz.ref index c5fda7aa..040d2be3 100644 --- a/tests/TERAPI-LZ/forces.xyz.ref +++ b/tests/TERAPI-LZ/forces.xyz.ref @@ -7,7 +7,15 @@ H -0.6280761008E-02 0.7518448370E-02 0.3313100155E-01 H -0.2782826117E-01 -0.1670370136E-02 0.3235792249E-01 H -0.1192180436E+00 0.1363320697E-01 -0.7406869050E-01 6 -net force: 0.18000E-09 -0.76000E-10 -0.10200E-09 torque force: -0.17562E-04 -0.46780E-04 0.29185E-05 +net force: -0.98000E-10 -0.95000E-10 0.11300E-09 torque force: 0.54503E-03 0.15043E-02 -0.71255E-04 +C 0.1394112435E+00 -0.1118998196E-01 -0.1461160381E+00 +N 0.3739084695E-01 -0.2565077705E-02 0.1496980461E+00 +H -0.2347502477E-01 -0.5726225634E-02 0.4997758573E-02 +H -0.6280761008E-02 0.7518448370E-02 0.3313100155E-01 +H -0.2782826117E-01 -0.1670370136E-02 0.3235792249E-01 +H -0.1192180436E+00 0.1363320697E-01 -0.7406869050E-01 + 6 +net force: 0.18000E-09 -0.76000E-10 -0.10200E-09 torque force: 0.15123E-02 0.37462E-03 0.13172E-03 C 0.1453320682E+00 -0.1833857157E-01 -0.7561297419E-01 N 0.6556333519E-01 0.2833881964E-02 0.8552960343E-01 H -0.1427369250E-01 -0.1469574481E-01 -0.3602639052E-02 @@ -15,7 +23,7 @@ H -0.1039579258E-01 0.1654956425E-01 0.3233472470E-01 H -0.5315088573E-01 -0.1246013689E-01 0.5272996316E-01 H -0.1330750324E+00 0.2611100698E-01 -0.9137867815E-01 6 -net force: 0.10000E-10 -0.41000E-10 0.47500E-09 torque force: 0.87201E-04 0.20489E-03 0.10174E-04 +net force: 0.10000E-10 -0.41000E-10 0.47500E-09 torque force: 0.57205E-04 -0.41423E-03 0.40398E-03 C 0.1548579790E+00 -0.5055664226E-02 -0.7698806528E-01 N 0.1036669994E+00 -0.1391908912E-01 0.6856667821E-01 H -0.1967027668E-01 0.1002265661E-01 0.2295511945E-02 diff --git a/tests/TERAPI-LZ/input.in b/tests/TERAPI-LZ/input.in index 1500dcae..9e75c49e 100644 --- a/tests/TERAPI-LZ/input.in +++ b/tests/TERAPI-LZ/input.in @@ -4,7 +4,7 @@ Energies and gradients based on simulation &general pot='_tera_', irandom=1104190577, -nstep=3, +nstep=4, dt=10., ipimd=5, diff --git a/tests/TERAPI-LZ/movie.xyz.ref b/tests/TERAPI-LZ/movie.xyz.ref index 94d3ac35..0bb9d976 100644 --- a/tests/TERAPI-LZ/movie.xyz.ref +++ b/tests/TERAPI-LZ/movie.xyz.ref @@ -16,9 +16,17 @@ H -0.80371675E+00 0.33577984E-01 0.18596712E+01 H -0.76143602E+00 0.32045533E-01 -0.57512841E+00 6 Time step: 3 Sim. Time [au] 30.00 -C -0.18785105E-01 -0.81627369E-02 -0.11114287E-01 -N -0.12420975E-01 -0.26501349E-02 0.13542082E+01 -H 0.99321113E+00 0.52801876E-01 -0.45026626E+00 -H 0.96071514E+00 0.19169248E-01 0.16567884E+01 -H -0.79729320E+00 0.29101275E-01 0.18392891E+01 -H -0.76070393E+00 0.32916251E-01 -0.57530014E+00 +C -0.18779626E-01 -0.81531535E-02 -0.11048396E-01 +N -0.12506342E-01 -0.26669538E-02 0.13541251E+01 +H 0.99303132E+00 0.52725753E-01 -0.45013188E+00 +H 0.96070211E+00 0.19337126E-01 0.16566918E+01 +H -0.79640481E+00 0.29105820E-01 0.18391089E+01 +H -0.76027853E+00 0.32939462E-01 -0.57478856E+00 + 6 +Time step: 4 Sim. Time [au] 40.00 +C -0.19295974E-01 -0.84675025E-02 -0.19376911E-01 +N -0.12738799E-01 -0.19155065E-02 0.13623543E+01 +H 0.99180206E+00 0.51979150E-01 -0.44899875E+00 +H 0.96853377E+00 0.16632624E-01 0.16622032E+01 +H -0.79081888E+00 0.24587783E-01 0.18197224E+01 +H -0.76308376E+00 0.34212593E-01 -0.57715709E+00 diff --git a/tests/TERAPI-LZ/pop.dat.ref b/tests/TERAPI-LZ/pop.dat.ref index 9adb5b4c..dbabf6f5 100644 --- a/tests/TERAPI-LZ/pop.dat.ref +++ b/tests/TERAPI-LZ/pop.dat.ref @@ -1,4 +1,5 @@ # Time[fs] CurrentState Populations Sum-of-Populations 0.24 3 0.00000 0.00000 1.00000 1.0000000 0.48 3 0.00000 0.00000 1.00000 1.0000000 - 0.73 2 0.00000 1.00000 0.00000 1.0000000 + 0.73 3 0.00000 0.00000 1.00000 1.0000000 + 0.97 2 0.00000 1.00000 0.00000 1.0000000 diff --git a/tests/TERAPI-LZ/velocities.xyz.ref b/tests/TERAPI-LZ/velocities.xyz.ref index 29441b79..7291cfe1 100644 --- a/tests/TERAPI-LZ/velocities.xyz.ref +++ b/tests/TERAPI-LZ/velocities.xyz.ref @@ -8,17 +8,25 @@ H 0.1608928990E-02 -0.8314806538E-03 -0.4149867289E-02 H 0.1191957499E-02 0.5763493425E-04 0.6688737067E-03 6 Time step: 2 -C -0.1928802948E-03 -0.5150233132E-04 -0.1445842411E-02 -N -0.7706894442E-04 0.1416691671E-03 0.1439734332E-02 -H -0.4599342984E-04 -0.1324692219E-03 0.1748465527E-03 -H 0.1521268390E-02 -0.5182551591E-03 0.7467483320E-03 -H 0.1388574163E-02 -0.8699316075E-03 -0.3918332048E-02 -H 0.5054351137E-03 0.1657841272E-03 0.2186698251E-03 +C -0.1942324077E-03 -0.4986983917E-04 -0.1461942888E-02 +N -0.8258577924E-04 0.1406119240E-03 0.1452300020E-02 +H -0.7103145576E-04 -0.1080619896E-03 0.1982493570E-03 +H 0.1532465928E-02 -0.5428300040E-03 0.7489151052E-03 +H 0.1457480330E-02 -0.8405712440E-03 -0.3973767029E-02 +H 0.5431417886E-03 0.1318304050E-03 0.2657725605E-03 6 Time step: 3 -C -0.1280667228E-03 -0.5539079233E-04 -0.1525343769E-02 -N -0.3883149049E-04 0.1405622540E-03 0.1510739454E-02 -H -0.1544546537E-03 -0.8198563715E-04 0.1927012084E-03 -H 0.1467752454E-02 -0.5740433409E-03 0.9449706261E-03 -H 0.9965950105E-03 -0.7953416846E-03 -0.3664819364E-02 -H -0.2442458167E-03 0.1582155808E-03 -0.2902812073E-03 +C -0.1292068227E-03 -0.5661314582E-04 -0.1512578173E-02 +N -0.6242493254E-04 0.1406645622E-03 0.1498363118E-02 +H -0.1737506418E-03 -0.1636328364E-03 0.2020456593E-03 +H 0.1487086849E-02 -0.4773378007E-03 0.9270558899E-03 +H 0.1237125503E-02 -0.8790221977E-03 -0.3742231788E-02 +H -0.1433805965E-03 0.2399795979E-03 -0.1844313212E-03 +6 +Time step: 4 +C -0.6221139923E-04 -0.6055789796E-04 -0.1591442578E-02 +N -0.2362765338E-04 0.1392772867E-03 0.1568507896E-02 +H -0.2858214413E-03 -0.1138146182E-03 0.2203759564E-03 +H 0.1429884434E-02 -0.5310243507E-03 0.1129162830E-02 +H 0.8383071925E-03 -0.8031515634E-03 -0.3476679632E-02 +H -0.9127038701E-03 0.2342605941E-03 -0.7054167345E-03