CPMD-code · foeroyingur · Jan 24, 2023
diff --git a/configure/MIMIC-LINUX-GCC b/configure/MIMIC-LINUX-GCC
@@ -0,0 +1,23 @@
+     IRAT=2
+     FC='mpif90'
+     CC='mpicc'
+     LD='mpif90'
+     CPP='cpp -P -traditional'
+     CPPFLAGS=' -D__Linux -D__HAS_FFT_FFTW3 -D__PARALLEL -D__HAS_SIZEOF '
+     if [ $debug ]; then
+       FFLAGS=' -g -pg -Og -ffree-line-length-none '
+       CFLAGS=' -g -pg -Og '
+     else
+       FFLAGS=' -O3 -march=native -mtune=native '
+       CFLAGS=' -O3 -march=native -mtune=native '
+     fi
+     if [ $omp ]; then
+       FFLAGS=${FFLAGS}' -fopenmp '
+       OMP3_DISABLED='false'
+       LIBS=' -L/usr/lib64 -llapack -lopenblaso -lfftw3_omp -lfftw3 -lm '
+     else
+       LIBS=' -L/usr/lib64 -llapack -lopenblas -lfftw3 -lm '
+     fi
+     LFLAGS=${LIBS}
+     FFLAGS=${FFLAGS}" -I/usr/include -fallow-argument-mismatch -ffree-line-length-none"
+     LFLAGS=${LFLAGS}" -L/usr/lib64 "
diff --git a/configure/MIMIC-LINUX-INTEL b/configure/MIMIC-LINUX-INTEL
@@ -0,0 +1,25 @@
+     IRAT=2
+     FC='mpiifort'
+     CC='mpiicc'
+     LD='mpiifort'
+     CPP='fpp'
+     CPPFLAGS=' -D__Linux -D__HAS_FFT_FFTW3 -D__PARALLEL -D__HAS_SIZEOF -D__HAS_BF_STREAM_IO '
+     AR='xiar -r'
+     RANLIB='ranlib'
+     if [ $debug ]; then
+       FFLAGS=' -g -O0 -check all -warn all -traceback '
+       CFLAGS=' -g -O0 -check all -warn all -traceback '
+     else
+       FFLAGS=' -xHost -O3 '
+       CFLAGS=' -xHost -O3 '
+     fi
+     if [ $omp ]; then
+       FFLAGS=${FFLAGS}' -qopenmp '
+       OMP3_DISABLED='false'
+       LIBS=' -qmkl=parallel -lm '
+     else
+       LIBS=' -qmkl=sequential -lm '
+     fi
+     LFLAGS=${LIBS}
+     FFLAGS=${FFLAGS}" -I/usr/include "
+     LFLAGS=${LFLAGS}" -L/usr/lib64 "
diff --git a/doc/manual/manual.tex b/doc/manual/manual.tex
diff --git a/scripts/configure.sh b/scripts/configure.sh
@@ -57,7 +57,8 @@ Description of options:
    -verbose    (-v) Display the name of files for the dependencies
    -coverage   (-c) With GCC compiler only, allows for specific configuration files,
                     to generate the code coverage/profiling during an execution
-   -qmmm            Generates a makefile for QMMM 
+   -mimic           Enable interface to MiMiC (requires MPI and that MiMiC is available)
+   -qmmm            Generates a makefile for QMMM
    -iphigenie       Support for external interface to iphigenie
    -omp             Enables the use of OMP instructions (if the config file allows that)
                     OMP3 is in general triggered by the config keyword OMP3_DISABLED,
@@ -130,6 +131,10 @@ do
     -disable_omp3)
       omp3=0
       ;;
+    -mimic|-m)
+      mimic=1
+      echo "** Enabling MiMiC interface (if MiMiC is available)" >&2
+      ;;
     -qmmm|-q)
       qmmm=1
       echo "** Enabling QM/MM (if Gromos and MM_Interface modules will be available)" >&2
@@ -241,6 +246,25 @@ fi
 
 CPPFLAGS_GROMOS='-DEWALD -DEWATCUT -DHAT_SHAPE -DUNPACKED_GRID'
 
+if [ $mimic ]; then
+  mkdir mimic_test
+  cd mimic_test
+  echo "program test" > test.f90
+  echo "use mimic_main" >> test.f90
+  echo "end program test" >> test.f90
+  ${FC} test.f90 ${FFLAGS} ${LFLAGS} -lmimic -lmimiccommf -lmimiccomm
+  if [ $? != 0 ]
+  then
+    cd ..
+    rm -r mimic_test
+    echo "MiMiC was not found on your system!" >&2
+    exit 1
+  fi
+  cd ..
+  rm -r mimic_test
+  CPPFLAGS=${CPPFLAGS}' -D__MIMIC'
+  LFLAGS=${LFLAGS}' -lmimic -lmimiccommf -lmimiccomm -lstdc++ '
+fi
 #QM/MM compilation setup
 if [ $qmmm ]; then
   if [ -f ${MOD_DIR}/QMMM_SOURCES ]; then
@@ -852,6 +876,11 @@ do
                SkipInclude["mpi"] = 0;
                SkipInclude["rhjsx.inc"] = 0;
                SkipInclude["uhjsx.inc"] = 0;
+               SkipInclude["mimic_precision"] = 0;
+               SkipInclude["mimic_constants"] = 0;
+               SkipInclude["mimic_types"] = 0;
+               SkipInclude["mimic_tensors"] = 0;
+               SkipInclude["mimic_main"] = 0;
                if (qmmm != 1) {
                   SkipInclude["coordsz"] = 0;
                }

diff --git a/src/SOURCES b/src/SOURCES
@@ -137,8 +137,8 @@ SRC_MODULES = kinds.mod.F90 machine.mod.F90 timer.mod.F90 error_handling.mod.F90
            meta_colvar_inp_utils.mod.F90 meta_exlagr_methods.mod.F90 meta_cv_utils.mod.F90 \
            meta_cv_qmmm_utils.mod.F90 tst2min_utils.mod.F90 tst2min_inp_utils.mod.F90 chain_dr_utils.mod.F90 meta_cell_utils.mod.F90 \
            meta_exl_mult_utils.mod.F90 meta_ex_mul_util_utils.mod.F90 meta_localizespin_utils.mod.F90 meta_colvar_util_utils.mod.F90 \
-           setbsstate_utils.mod.F90 io_utils.mod.F90 atoms_utils.mod.F90 dynit_utils.mod.F90 shake_utils.mod.F90 \
-           rattle_utils.mod.F90 resetac_utils.mod.F90 dispp_utils.mod.F90 \
+           setbsstate_utils.mod.F90 io_utils.mod.F90 atoms_utils.mod.F90 dynit_utils.mod.F90 constraint.mod.F90 constraint_utils.mod.F90 \
+           shake_utils.mod.F90 rattle_utils.mod.F90 resetac_utils.mod.F90 dispp_utils.mod.F90 \
            noseinit_utils.mod.F90 nospinit_utils.mod.F90 noseng_utils.mod.F90 nosepa_utils.mod.F90 noseup_utils.mod.F90 \
            enosmove_utils.mod.F90 pnosmove_utils.mod.F90 \
            vdw_utils.mod.F90 chksym_utils.mod.F90 symtrz_utils.mod.F90 multtb_utils.mod.F90 molsym_utils.mod.F90 \
@@ -269,4 +269,4 @@ SRC_MODULES = kinds.mod.F90 machine.mod.F90 timer.mod.F90 error_handling.mod.F90
            bicanonicalCpmd.mod.F90 bicanonicalConfig.mod.F90 bicanonicalInputReader.mod.F90 bicanonicalCalculationConfig.mod.F90 bicanonicalCalculation.mod.F90 \
           pi_prpt_utils.mod.F90 pi_npt_cpmd_utils.mod.F90 pi_stress_utils.mod.F90 pi_npt_bomd_utils.mod.F90 \
           nvml_interfaces.mod.F90 nvml_types.mod.F90 nvml_utils.mod.F90 mts_utils.mod.F90 interface_utils.mod.F90 \
-          dftd3_driver.mod.F90 
+          dftd3_driver.mod.F90 mimic_wrapper.mod.F90
diff --git a/src/anneal_utils.mod.F90 b/src/anneal_utils.mod.F90
@@ -5,6 +5,7 @@ MODULE anneal_utils
                                              s_ekinpp
   USE ions,                            ONLY: ions1
   USE kinds,                           ONLY: real_8
+  USE mimic_wrapper,                   ONLY: mimic_control
   USE nose,                            ONLY: glib
   USE parac,                           ONLY: paral
   USE pimd,                            ONLY: ipcurr,&
@@ -51,19 +52,48 @@ SUBROUTINE anneal(velp,cm,nstate,htvel)
     ! ==  ANNEALING (IONS)  Fixed rescaling factor (anner)            ==
     ! ==--------------------------------------------------------------==
     IF (cntl%annei.AND.(.NOT.skipanic)) THEN
-       alfap=cntr%anneri**(0.25_real_8)
+       IF (cntl%anneal_dual) THEN
+          alfap = cntr%anneal_factors(1)**(0.25_real_8)
 #if defined(__VECTOR)
-       !$omp parallel do private(I,IS,IA)
+          !$omp parallel do private(I,IS,IA)
 #else
-       !$omp parallel do private(I,IS,IA) schedule(static)
+          !$omp parallel do private(I,IS,IA) schedule(static)
 #endif
-       DO i=1,ions1%nat
-          ia=iatpt(1,i)
-          is=iatpt(2,i)
-          velp(1,ia,is)=alfap*velp(1,ia,is)
-          velp(2,ia,is)=alfap*velp(2,ia,is)
-          velp(3,ia,is)=alfap*velp(3,ia,is)
-       ENDDO
+          DO i = 1, mimic_control%num_quantum_atoms
+           ia = iatpt(1,i)
+           is = iatpt(2,i)
+           velp(1,ia,is) = alfap * velp(1,ia,is)
+           velp(2,ia,is) = alfap * velp(2,ia,is)
+           velp(3,ia,is) = alfap * velp(3,ia,is)
+          ENDDO
+          alfap = cntr%anneal_factors(2)**(0.25_real_8)
+#if defined(__VECTOR)
+          !$omp parallel do private(I,IS,IA)
+#else
+          !$omp parallel do private(I,IS,IA) schedule(static)
+#endif
+          DO i = mimic_control%num_quantum_atoms + 1, mimic_control%num_atoms
+             ia = iatpt(1,i)
+             is = iatpt(2,i)
+             velp(1,ia,is) = alfap * velp(1,ia,is)
+             velp(2,ia,is) = alfap * velp(2,ia,is)
+             velp(3,ia,is) = alfap * velp(3,ia,is)
+          ENDDO
+       ELSE
+          alfap=cntr%anneri**(0.25_real_8)
+#if defined(__VECTOR)
+          !$omp parallel do private(I,IS,IA)
+#else
+          !$omp parallel do private(I,IS,IA) schedule(static)
+#endif
+          DO i=1,ions1%nat
+             ia=iatpt(1,i)
+             is=iatpt(2,i)
+             velp(1,ia,is)=alfap*velp(1,ia,is)
+             velp(2,ia,is)=alfap*velp(2,ia,is)
+             velp(3,ia,is)=alfap*velp(3,ia,is)
+          ENDDO
+       END IF
     ENDIF
     ! ==--------------------------------------------------------------==
     ! ==  ANNEALING (ELECTRONS)  Fixed rescaling factor (anner)       ==

diff --git a/src/constraint.mod.F90 b/src/constraint.mod.F90
@@ -0,0 +1,126 @@
+module constraint
+    USE kinds,                           ONLY: real_8
+
+    implicit none
+
+    !> Type used to store sparse constraint matrix
+    !> @author V. Bolnykh - RWTH Aachen/Cyprus Institute
+    type constraint_matrix
+        ! Values stored in a sparse matrix
+        real(real_8), dimension(:), allocatable :: vals
+        ! Number of non-zero elements of the current row
+        integer, dimension(:), allocatable :: nz_row
+        ! Index of a non-zero element in the row
+        integer, dimension(:), allocatable :: r_index
+        ! IDs of atoms in a constraint
+        integer, dimension(:, :), allocatable :: atom_id
+        ! Species and atom IDs in the constraint (needed for TAU
+        ! mapping)
+        integer, dimension(:, :, :), allocatable :: tau_map
+        ! Reference value for a constraint
+        real(real_8), dimension(:), allocatable :: ref
+
+        contains
+        procedure :: mat_vec
+        generic :: operator(*) => mat_vec
+    end type constraint_matrix
+
+    !> Interface of the constraint_matrix constructor
+    interface constraint_matrix
+        module procedure new_matrix
+    end interface
+
+contains
+
+    !> Matrix-vector multiplication
+    function mat_vec(m, v) result(r)
+
+        !> input matrix
+        class(constraint_matrix), intent(in) :: m
+        !> input vector
+        real(real_8), dimension(:), intent(in) :: v
+
+        !> resulting vector
+        real(real_8), dimension(:), allocatable :: r
+
+        integer :: i, j
+
+        allocate(r(size(v)))
+
+        r = 0.0_real_8
+
+        !$OMP PARALLEL DO PRIVATE(i, j)
+        do i = 1, size(m%nz_row) - 1
+            do j = m%nz_row(i - 1) + 1, m%nz_row(i)
+                r(i) = r(i) + m%vals(j) * v(m%r_index(j))
+            end do
+        end do
+        !$OMP END PARALLEL DO
+
+    end function
+
+    !> Constructor of the sparse matrix
+    function new_matrix(vals, nz_row, r_index, atom_id, tau_map, ref)
+
+        real(real_8), dimension(:), intent(in) :: vals
+        integer, dimension(0:), intent(in) :: nz_row
+        integer, dimension(:), intent(in) :: r_index
+        integer, dimension(:,:), intent(in) :: atom_id
+        integer, dimension(:,:,:), intent(in) :: tau_map
+        real(real_8), dimension(:), intent(in) :: ref
+
+        type(constraint_matrix) :: new_matrix
+
+        integer :: i, j
+
+        allocate(new_matrix%vals(size(vals)))
+        allocate(new_matrix%nz_row(0:size(nz_row) - 1))
+        allocate(new_matrix%r_index(size(r_index)))
+        allocate(new_matrix%atom_id(size(atom_id, 1), size(atom_id, 2)))
+        allocate(new_matrix%tau_map(size(tau_map, 1), size(tau_map, 2), &
+                 size(tau_map, 3)))
+        allocate(new_matrix%ref(size(ref)))
+
+        !$OMP PARALLEL PRIVATE(i, j)
+        !$OMP DO
+        do i = 1, size(vals)
+            new_matrix%vals(i) = vals(i)
+        end do
+        !$OMP END DO
+
+        !$OMP DO
+        do i = 0, size(nz_row) - 1
+            new_matrix%nz_row(i) = nz_row(i)
+        end do
+        !$OMP END DO
+
+        !$OMP DO
+        do i = 1, size(r_index)
+            new_matrix%r_index(i) = r_index(i)
+        end do
+        !$OMP END DO
+
+        !$OMP DO
+        do i = 1, size(atom_id, 2)
+            new_matrix%atom_id(:, i) = atom_id(:, i)
+        end do
+        !$OMP END DO
+
+        !$OMP DO
+        do i = 1, size(tau_map, 3)
+            do j = 1, size(tau_map, 2)
+                new_matrix%tau_map(:, j, i) = tau_map(:, j, i)
+            end do
+        end do
+        !$OMP END DO
+
+        !$OMP DO
+        do i = 1, size(ref)
+            new_matrix%ref(i) = ref(i)
+        end do
+        !$OMP END DO
+        !$OMP END PARALLEL
+
+    end function
+
+end module constraint