Merge pull request #23 from SebastianHavens/master

Adding the fortran implementation of the WRDF potential (originally published in Phys. Chem. Chem. Phys., 2020, 22,10624)

Makefile

@@ -1,6 +1,6 @@
 include Makefile.arch
 
-F90_MODEL_UTILS = example_mat_mod.F90 example_LJ_params_mod.F90 example_bead_spring_polymer_params_mod.F90 example_Jagla_params_mod.F90 example_CollapsingSpheres_params_mod.F90
+F90_MODEL_UTILS = example_mat_mod.F90 example_LJ_params_mod.F90 example_bead_spring_polymer_params_mod.F90 example_Jagla_params_mod.F90 example_CollapsingSpheres_params_mod.F90 Wang_LJ_params_mod.F90
 
 F90_MODELS = $(wildcard *_model.F90)
 

Wang_LJ_model.F90

@@ -0,0 +1,390 @@
+! publically accessible things required for interface to pymatnest
+!
+! subroutine ll_init_model(N_params, params) 
+!    integer :: N_params ! number of parameters
+!    double precision :: params(N_params) ! list of parameters
+!
+!    initializes potential
+!
+! subroutine ll_init_config(N, Z, pos, cell, Emax) 
+!    integer :: N ! number of atoms
+!    integer :: Z(N) ! atomic numbers of atoms
+!    double precision :: pos(3,N), cell(3,3) ! positions, cell vectors
+!    double precision :: Emax ! maximum energy for config acceptance
+!
+!    initializes a configuration with energy < Emax
+!    config will be tested for failure after return
+!
+! double precision function ll_eval_energy(N, Z, pos, n_extra_data, extra_data, cell)
+!    integer :: N ! number of atoms
+!    double precision :: pos(3,N), cell(3,3) ! positions, cell vectors
+!    integer :: n_extra_data ! width of extra data array
+!    double precision :: extra_data(n_extra_data, N) ! extra data on output
+!
+!    evaluates energy of a config, sets extra_data, returns energy
+!
+! integer function ll_move_atom_1(N, pos, n_extra_data, extra_data, cell, d_i, d_pos, dEmax, dE)
+!    integer :: N ! number of atoms
+!    double precision :: pos(3,N), cell(3,3) ! positions, cell vectors, on output updated (pos only) to be consistent with acceptance/rejection
+!    integer :: n_extra_data ! width of extra data array
+!    double precision :: extra_data(n_extra_data, N) ! extra data on input, on output updated to be consistent with acceptance/rejection
+!    integer :: d_i ! index of atom to be perturbed, 1-based (called from fortran_MC())
+!    double precision :: d_pos(3) ! displacement of perturbed atom
+!    double precision :: dEmax ! maximum change in energy for move acceptance
+!    double precision :: dE ! on output actual change in energy, 0.0 if move is rejected
+!
+!    moves an atom if dE < dEmax
+!    if move is accepted, updates pos, extra_data, sets dE
+!    if move is rejected, nothing is updated, dE set to 0.0
+!    returns 1 for accept, 0 for reject
+!
+! double precision function ll_eval_forces(N, pos, n_extra_data, extra_data, cell, forces)
+!    integer :: N ! number of atoms
+!    double precision :: pos(3,N), cell(3,3), forces(3,N) ! positions, cell vectors, forces
+!    integer :: n_extra_data ! width of extra data array
+!    double precision :: extra_data(n_extra_data, N) ! extra data on output
+!
+!    evaluates forces, sets extra_data
+!    returns energy
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+subroutine ll_init_model(N_params, params)
+use Wang_LJ_params_mod
+implicit none
+   integer :: N_params
+   double precision :: params(N_params)
+
+
+      epsilon(1,1) = 1.0
+      epsilon(2,2) = 1.0
+      epsilon(1,2) = 1.0
+      epsilon(2,1) = epsilon(1,2)
+
+      sigma(1,1) = 1.0
+      sigma(2,2) = 1.0
+      sigma(1,2) = (sigma(1,1)+sigma(2,2))/2.0
+      sigma(2,1) = sigma(1,2)
+
+      if (N_params==1) then
+
+      mu = 1
+      nu = 1
+
+      cutoff = 2.0
+      cutoff_sq = cutoff*cutoff
+
+      alpha = 1.0
+
+   else
+
+      mu = int(params(1))
+      nu = int(params(2))
+
+      cutoff = params(3)*sigma
+      cutoff_sq = cutoff*cutoff
+
+
+      write(*,*) "User defined parameters:"
+      write(*,*) "(1)-(1) epsilon = ", epsilon(1,1)," (2)-(2) epsilon = ", epsilon(2,2)
+      write(*,*) "(1)-(1) sigma = ", sigma(1,1)," (2)-(2) sigma = ", sigma(2,2)
+      write(*,*) "Mixed term LJ parameters are calculated using the", &
+      &" Lorenz-Berthelot rule."
+      write(*,*) "mu = ", mu, " nu = ", nu
+      write(*,*) "cutoff (1) = ", cutoff(1,1), " cutoff (2) = ", cutoff(2,2)
+   end if
+
+   alpha = 2.0*(cutoff_sq/(sigma**2))*((3/(2*(((cutoff_sq/(sigma**2)))-1)))**3)
+
+
+
+end subroutine ll_init_model
+
+subroutine ll_init_config(N, Z, pos, cell, Emax)
+implicit none
+   integer :: N
+   integer :: Z(N)
+   double precision :: pos(3,N), cell(3,3)
+   double precision :: Emax
+   return
+end subroutine ll_init_config
+
+double precision function ll_eval_energy(N, Z, pos, n_extra_data, extra_data, cell)
+use example_mat_mod
+use Wang_LJ_params_mod
+implicit none
+   integer :: N
+   integer :: Z(N)
+   double precision :: pos(3,N), cell(3,3)
+   integer :: n_extra_data
+   double precision :: extra_data(n_extra_data, N)
+
+   integer :: i, j, Z_i, Z_j
+   double precision :: dr(3), dr_mag, dr_mag_sq, dr_l(3), dr_l0(3), pos_l(3,N)
+
+   double precision :: cell_inv(3,3), E_term
+   integer :: dj1, dj2, dj3
+
+   integer :: n_images
+   double precision cell_height(3), v_norm_hat(3)
+
+   call matrix3x3_inverse(cell, cell_inv)
+   ! into lattice coodinates 
+   pos_l = matmul(cell_inv, pos)
+
+   if (n_extra_data == 1) extra_data = 0.0
+
+   do i=1, 3
+      v_norm_hat = cell(:,mod(i,3)+1) .cross. cell(:,mod(i+1,3)+1)
+      v_norm_hat = v_norm_hat / sqrt(sum(v_norm_hat**2))
+      cell_height(i) = abs(sum(v_norm_hat*cell(:,i)))
+   end do
+   n_images = ceiling(maxval(cutoff)/minval(cell_height))
+
+   ll_eval_energy = 0.0
+   do i=1, N
+   Z_i = Z(i)
+   do j=i, N
+      Z_j = Z(j)
+      dr_l0 = pos_l(:,i)-pos_l(:,j)
+      dr_l0 = dr_l0 - floor(dr_l0+0.5)
+      do dj1=-n_images,n_images
+      dr_l(1) = dr_l0(1) + real(dj1, 8)
+      do dj2=-n_images,n_images
+      dr_l(2) = dr_l0(2) + real(dj2, 8)
+      do dj3=-n_images,n_images
+      dr_l(3) = dr_l0(3) + real(dj3, 8)
+	 if (i == j .and. dj1 == 0 .and. dj2 == 0 .and. dj3 == 0) cycle
+
+	 dr(1) = sum(cell(1,:)*dr_l)
+	 dr(2) = sum(cell(2,:)*dr_l)
+	 dr(3) = sum(cell(3,:)*dr_l)
+	 dr_mag_sq = sum(dr*dr)
+	 if (dr_mag_sq < cutoff_sq(Z_i,Z_j)) then
+	    dr_mag = sqrt(dr_mag_sq)
+	    E_term = epsilon(Z_i,Z_j)*alpha(Z_i,Z_j)*(((sigma(Z_i,Z_j)/dr_mag)**(2*mu) - 1.0) * &
+       ((cutoff(Z_i,Z_j)/dr_mag)**(2*mu)-1.0)**(2*nu))
+	    if (i == j) E_term = E_term * 0.5
+	    ll_eval_energy = ll_eval_energy + E_term
+
+	    if (n_extra_data == 1) then
+	       extra_data(1,i) = extra_data(1,i) + 0.5*E_term
+	       extra_data(1,j) = extra_data(1,j) + 0.5*E_term
+	    endif
+
+	 endif
+      end do
+      end do
+      end do
+   end do
+   end do
+
+end function ll_eval_energy
+
+integer function ll_move_atom_1(N, Z, pos, n_extra_data, extra_data, cell, d_i, d_pos, dEmax, dE)
+use example_mat_mod
+use Wang_LJ_params_mod
+implicit none
+   integer :: N
+   integer :: Z(N)
+   double precision :: pos(3,N), cell(3,3)
+   integer :: n_extra_data
+   double precision :: extra_data(n_extra_data, N)
+   integer :: d_i
+   double precision :: d_pos(3)
+   double precision :: dEmax, dE
+
+   integer :: i, j, Z_i, Z_j
+   double precision :: dr(3), drp(3), dr_l(3), drp_l(3), dr_l0(3), drp_l0(3), dr_mag, drp_mag, &
+		       dr_mag_sq, drp_mag_sq, pos_l(3,N), d_pos_l(3)
+
+   double precision :: cell_inv(3,3) 
+   integer :: dj1, dj2, dj3
+
+   double precision, allocatable, save :: new_extra_data(:,:)
+
+   integer n_images
+   double precision cell_height(3), v_norm_hat(3)
+
+   do i=1, 3
+      v_norm_hat = cell(:,mod(i,3)+1) .cross. cell(:,mod(i+1,3)+1)
+      v_norm_hat = v_norm_hat / sqrt(sum(v_norm_hat**2))
+      cell_height(i) = abs(sum(v_norm_hat*cell(:,i)))
+   end do
+   n_images = ceiling(maxval(cutoff)/minval(cell_height))
+
+   call matrix3x3_inverse(cell, cell_inv)
+   ! into lattice coodinates 
+   do i=1, N
+       pos_l(1,i) = sum(cell_inv(1,:)*pos(:,i))
+       pos_l(2,i) = sum(cell_inv(2,:)*pos(:,i))
+       pos_l(3,i) = sum(cell_inv(3,:)*pos(:,i))
+   end do
+   d_pos_l(1) = sum(cell_inv(1,:)*d_pos(:))
+   d_pos_l(2) = sum(cell_inv(2,:)*d_pos(:))
+   d_pos_l(3) = sum(cell_inv(3,:)*d_pos(:))
+
+
+   if (n_extra_data == 1 .and. allocated(new_extra_data)) then
+      if (any(shape(new_extra_data) /= shape(extra_data))) then
+	 deallocate(new_extra_data)
+      endif
+   endif
+   if (n_extra_data == 1 .and. .not. allocated(new_extra_data)) then
+      allocate(new_extra_data(n_extra_data, N))
+   endif
+
+   if (n_extra_data == 1) new_extra_data = extra_data
+
+   dE = 0.0
+   i=d_i
+   Z_i = Z(i)
+   do j=1,N
+      if (j == i) cycle
+      Z_j = Z(j)
+
+      dr_l0 = pos_l(:,i) - pos_l(:,j)
+      dr_l0 = dr_l0 - floor(dr_l0+0.5)
+
+      drp_l0 = pos_l(:,i)+d_pos_l(:) - pos_l(:,j)
+      drp_l0 = drp_l0 - floor(drp_l0+0.5)
+
+      do dj1=-n_images,n_images
+      dr_l(1) = dr_l0(1) + real(dj1, 8)
+      drp_l(1) = drp_l0(1) + real(dj1, 8)
+      do dj2=-n_images,n_images
+      dr_l(2) = dr_l0(2) + real(dj2, 8)
+      drp_l(2) = drp_l0(2) + real(dj2, 8)
+      do dj3=-n_images,n_images
+      dr_l(3) = dr_l0(3) + real(dj3, 8)
+      drp_l(3) = drp_l0(3) + real(dj3, 8)
+
+         dr(1) = sum(cell(1,:)*dr_l)
+         dr(2) = sum(cell(2,:)*dr_l)
+         dr(3) = sum(cell(3,:)*dr_l)
+         drp(1) = sum(cell(1,:)*drp_l)
+         drp(2) = sum(cell(2,:)*drp_l)
+         drp(3) = sum(cell(3,:)*drp_l)
+	 dr_mag_sq = sum(dr*dr)
+	 drp_mag_sq = sum(drp*drp)
+
+	 if (dr_mag_sq < cutoff_sq(Z_i,Z_j)) then
+	    dr_mag = sqrt(dr_mag_sq)
+	    dE = dE -  epsilon(Z_i,Z_j)*alpha(Z_i,Z_j)*(((sigma(Z_i,Z_j)/dr_mag)**(2*mu) - 1.0) &
+            * ((cutoff(Z_i,Z_j)/dr_mag)**(2*mu)-1.0)**(2*nu))
+	    if (n_extra_data == 1) then
+         new_extra_data(1,i) = new_extra_data(1,i) - 0.5*epsilon(Z_i,Z_j)*alpha(Z_i,Z_j)* &
+         (((sigma(Z_i,Z_j)/dr_mag)**(2*mu) - 1.0) * ((cutoff(Z_i,Z_j)/dr_mag)**(2*mu)-1.0)**(2*nu))
+         new_extra_data(1,j) = new_extra_data(1,j) - 0.5*epsilon(Z_i,Z_j)*alpha(Z_i,Z_j)* &
+         (((sigma(Z_i,Z_j)/dr_mag)**(2*mu) - 1.0) * ((cutoff(Z_i,Z_j)/dr_mag)**(2*mu)-1.0)**(2*nu))
+	    endif
+	 endif
+	 if (drp_mag_sq < cutoff_sq(Z_i,Z_j)) then
+	    drp_mag = sqrt(drp_mag_sq)
+	    dE = dE + epsilon(Z_i,Z_j)*alpha(Z_i,Z_j)*(((sigma(Z_i,Z_j)/drp_mag)**(2*mu) - 1.0) * &
+            ((cutoff(Z_i,Z_j)/drp_mag)**(2*mu)-1.0)**(2*nu))
+	    if (n_extra_data == 1) then
+	       new_extra_data(1,i) = new_extra_data(1,i) + 0.5*epsilon(Z_i,Z_j)*alpha(Z_i,Z_j)*(((sigma(Z_i,Z_j)/dr_mag)**(2*mu) - 1.0) &
+                                     * ((cutoff(Z_i,Z_j)/dr_mag)**(2*mu)-1.0)**(2*nu))
+	       new_extra_data(1,j) = new_extra_data(1,j) + 0.5*epsilon(Z_i,Z_j)*alpha(Z_i,Z_j)*(((sigma(Z_i,Z_j)/dr_mag)**(2*mu) - 1.0) &
+                                     * ((cutoff(Z_i,Z_j)/dr_mag)**(2*mu)-1.0)**(2*nu))
+	    endif
+	 endif
+
+      end do
+      end do
+      end do
+   end do
+
+   if (dE < dEmax) then ! accept
+      pos(:,i) = pos(:,i) + d_pos(:)
+      if (n_extra_data == 1) extra_data = new_extra_data
+      ll_move_atom_1 = 1
+   else ! reject
+      dE = 0.0
+      ll_move_atom_1 = 0
+   endif
+
+end function ll_move_atom_1
+
+function ll_eval_forces(N, Z, pos, n_extra_data, extra_data, cell, forces) result(energy)
+use example_mat_mod
+use Wang_LJ_params_mod
+implicit none
+   integer :: N
+   integer :: Z(N)
+   double precision :: pos(3,N), cell(3,3), forces(3,N)
+   integer :: n_extra_data
+   double precision :: extra_data(n_extra_data, N)
+   double precision :: energy ! result
+
+   integer :: i, j, Z_i, Z_j
+   double precision :: dr(3), dr_mag, dr_mag_sq, dr_l(3), dr_l0(3), pos_l(3,N)
+   double precision :: cell_inv(3,3), E_term
+   integer :: dj1, dj2, dj3
+
+   integer n_images
+   double precision cell_height(3), v_norm_hat(3)
+
+   do i=1, 3
+      v_norm_hat = cell(:,mod(i,3)+1) .cross. cell(:,mod(i+1,3)+1)
+      v_norm_hat = v_norm_hat / sqrt(sum(v_norm_hat**2))
+      cell_height(i) = abs(sum(v_norm_hat*cell(:,i)))
+   end do
+   n_images = ceiling(maxval(cutoff)/minval(cell_height))
+
+   call matrix3x3_inverse(cell, cell_inv)
+   do i=1, N
+       pos_l(1,i) = sum(cell_inv(1,:)*pos(:,i))
+       pos_l(2,i) = sum(cell_inv(2,:)*pos(:,i))
+       pos_l(3,i) = sum(cell_inv(3,:)*pos(:,i))
+   end do
+
+   if (n_extra_data == 1) extra_data = 0.0
+
+   energy = 0.0
+   forces = 0.0
+   do i=1, N
+   Z_i = Z(i)
+   do j=i, N
+      Z_j = Z(j)
+
+      dr_l0 = pos_l(:,i) - pos_l(:,j)
+      dr_l0 = dr_l0 - floor(dr_l0+0.5)
+      do dj1=-n_images,n_images
+      dr_l(1) = dr_l0(1) + real(dj1, 8)
+      do dj2=-n_images,n_images
+      dr_l(2) = dr_l0(2) + real(dj2, 8)
+      do dj3=-n_images,n_images
+      dr_l(3) = dr_l0(3) + real(dj3, 8)
+      if (i == j .and. dj1 == 0 .and. dj2 == 0 .and. dj3 == 0) cycle
+
+         dr(1) = sum(cell(1,:)*dr_l)
+         dr(2) = sum(cell(2,:)*dr_l)
+         dr(3) = sum(cell(3,:)*dr_l)
+	 dr_mag_sq = sum(dr*dr)
+	 if (dr_mag_sq < cutoff_sq(Z_i,Z_j)) then
+	    dr_mag = sqrt(dr_mag_sq)
+	    E_term = epsilon(Z_i,Z_j)*alpha(Z_i,Z_j)*(((sigma(Z_i,Z_j)/dr_mag)**(2*mu) - 1.0) * &
+                ((cutoff(Z_i,Z_j)/dr_mag)**(2*mu)-1.0)**(2*nu))
+	    if (i == j) E_term = E_term * 0.5
+	    energy = energy + E_term
+	    if (n_extra_data == 1) then
+	       extra_data(1,i) = extra_data(1,i) + 0.5*E_term
+	       extra_data(1,j) = extra_data(1,j) + 0.5*E_term
+	    endif
+	    if (i /= j) then
+	       forces(:,i) = forces(:,i) - epsilon(Z_i,Z_j)*(-12.0*sigma(Z_i,Z_j)**12/dr_mag**13 + &
+                             6.0*sigma(Z_i,Z_j)**6/dr_mag**7)*(dr/dr_mag)
+	       forces(:,j) = forces(:,j) + epsilon(Z_i,Z_j)*(-12.0*sigma(Z_i,Z_j)**12/dr_mag**13 + &
+                             6.0*sigma(Z_i,Z_j)**6/dr_mag**7)*(dr/dr_mag) !!!!! needs to be fixed
+	    endif
+	 endif
+
+      end do
+      end do
+      end do
+   end do
+   end do
+
+end function ll_eval_forces