diff --git a/src/Makefile b/src/Makefile index c1d6422b..e2baf631 100755 --- a/src/Makefile +++ b/src/Makefile @@ -1,6 +1,6 @@ F_OBJS := constants.o fortran_interfaces.o error.o modules.o mpi_wrapper.o files.o utils.o io.o random.o arrays.o qmmm.o fftw_interface.o \ shake.o nosehoover.o gle.o transform.o potentials.o force_spline.o estimators.o ekin.o vinit.o plumed.o \ - remd.o force_bound.o water.o h2o_schwenke.o h2o_cvrqd.o force_h2o.o force_cp2k.o sh_integ.o surfacehop.o landau_zener.o\ + remd.o force_bound.o water.o h2o_schwenke.o h2o_cvrqd.o force_h2o.o force_cp2k.o sh_integ.o surfacehop.o landau_zener.o potentials_sh.o\ force_mm.o tera_mpi_api.o force_abin.o force_tcpb.o force_tera.o force_terash.o en_restraint.o analyze_ext_template.o geom_analysis.o analysis.o \ minimizer.o mdstep.o forces.o cmdline.o init.o diff --git a/src/forces.F90 b/src/forces.F90 index 4e527c6e..5af786cb 100644 --- a/src/forces.F90 +++ b/src/forces.F90 @@ -133,6 +133,7 @@ subroutine force_wrapper(x, y, z, fx, fy, fz, e_pot, chpot, walkmax) use mod_sbc, only: force_sbc, isbc use mod_plumed, only: iplumed, force_plumed use mod_potentials, only: force_harmonic_rotor, force_harmonic_oscillator, force_morse, force_doublewell + use mod_potentials_sh, only: force_nai use mod_splined_grid, only: force_splined_grid use mod_cp2k, only: force_cp2k use mod_shell_interface, only: force_abin @@ -173,6 +174,8 @@ subroutine force_wrapper(x, y, z, fx, fy, fz, e_pot, chpot, walkmax) call force_cp2k(x, y, z, fx, fy, fz, eclas, walkmax) case ("_tcpb_") call force_tcpb(x, y, z, fx, fy, fz, eclas, walkmax) + case ("_nai_") + call force_nai(x, y, z, fx, fy, fz, eclas) case ("_tera_") if (ipimd == 2 .or. ipimd == 5) then call force_terash(x, y, z, fx, fy, fz, eclas) diff --git a/src/init.F90 b/src/init.F90 index d8496170..4a6f45ed 100644 --- a/src/init.F90 +++ b/src/init.F90 @@ -40,7 +40,8 @@ subroutine init(dt) use mod_nhc use mod_estimators use mod_potentials - use mod_sh_integ, only: phase + use mod_potentials_sh + use mod_sh_integ, only: phase, nstate use mod_sh, only: read_sh_input, print_sh_input use mod_lz use mod_qmmm, only: natqm, natmm @@ -518,6 +519,9 @@ subroutine init(dt) if (pot == '_mm_' .or. pot_ref == '_mm_') then call initialize_mm(natom, atnames, mm_types, q, LJ_rmin, LJ_eps) end if + if (pot == '_nai_' .or. pot_ref == '_nai_') then + call nai_init(natom, nwalk, ipimd, nstate) + end if if (my_rank == 0) then call print_simulation_parameters() diff --git a/src/potentials_sh.F90 b/src/potentials_sh.F90 new file mode 100644 index 00000000..0483b697 --- /dev/null +++ b/src/potentials_sh.F90 @@ -0,0 +1,170 @@ +! Various analytical potentials for surface hopping: +! - NaI potential and couplings in adiabatic basis + +! Created by Jiri Janos + +module mod_potentials_sh + use mod_const, only: DP + implicit none + public + private :: nai + + ! We use derived types to encapsulate potential parameters + ! https://fortran-lang.org/learn/quickstart/derived_types + + ! Parameters for the NaI model as defined in the following articles + ! https://doi.org/10.1063/1.4919780 + ! https://doi.org/10.1063/1.456377 + ! These articles contain diabatic basis while here we use adiabatic. In this code, we first calculate the diabatic quantities and + ! then we convert them to adiabatic using a simple diagonalization of 2 states. The equations for diabatic quantites can be found + ! in the code or in appendix of this article: https://doi.org/10.1063/5.0071376 (sign is not correct) or equation 1 of this paper + ! https://doi.org/10.1063/1.1377030. + type :: nai_params + ! Diabatic state VX parameters + real(DP) :: a2 = 2760D0 + real(DP) :: b2 = 2.398D0 + real(DP) :: c2 = 11.3D0 + real(DP) :: lp = 0.408D0 + real(DP) :: lm = 6.431D0 + real(DP) :: rho = 0.3489D0 + real(DP) :: de0 = 2.075D0 + real(DP) :: e2 = 14.399613877582553D0 ! elementary charge in eV/angs units + ! Diabatic state VA parameters + real(DP) :: a1 = 0.813D0 + real(DP) :: beta1 = 4.08D0 + real(DP) :: r0 = 2.67D0 + ! Diabatic coupling VXA parameters + real(DP) :: a12 = 0.055D0 + real(DP) :: beta12 = 0.6931D0 + real(DP) :: rx = 6.93D0 + end type + type(nai_params) :: nai + save +contains + + ! NaI potential + subroutine nai_init(natom, nwalk, ipimd, nstate) + use mod_error, only: fatal_error + use mod_utils, only: real_positive + integer, intent(in) :: natom, nwalk, ipimd, nstate + + if (natom /= 2) then + call fatal_error(__FILE__, __LINE__, & + & 'NaI potential is only for 2 particles.') + end if + + if (nwalk /= 1) then + call fatal_error(__FILE__, __LINE__, & + & 'NaI model requires only 1 walker.') + end if + + if (ipimd /= 2) then + call fatal_error(__FILE__, __LINE__, & + & 'NaI model works only with SH dynamics.') + end if + + if (nstate /= 2) then + call fatal_error(__FILE__, __LINE__, & + & 'NaI model is implemented for 2 states only.') + end if + + end subroutine nai_init + + subroutine force_nai(x, y, z, fx, fy, fz, eclas) + use mod_sh, only: en_array, istate, nacx, nacy, nacz + use mod_const, only: ANG, AUTOEV + real(DP), intent(in) :: x(:, :), y(:, :), z(:, :) + real(DP), intent(out) :: fx(:, :), fy(:, :), fz(:, :) + real(DP), intent(out) :: eclas + real(DP) :: VX, VA, VXA, dVX, dVA, dVXA ! diabatic hamiltonian and its derivatives + real(DP) :: E1, E2, d12, dE1, dE2 ! adiabatic hamiltonian and derivatives of energies + real(DP) :: r, fr, dx, dy, dz + + ! NOTE: The original potential is defined in diabatic basis. For ABIN's purposes, we need to transfer to adiabatic basis, + ! which can be easily done for two states. However, the adiabatic formulas are very long and complicated to both code and + ! read. Therefore, we calculate the diabatic quantities and their derivatives and then construct the adiabatic states and + ! couplings from diabatic ones. It should be easier to read and also more efficient. Note that the diabatic potential is + ! in eV and Angstrom so conversions are necessary. + + ! distance between atoms + dx = x(2, 1) - x(1, 1) + dy = y(2, 1) - y(1, 1) + dz = z(2, 1) - z(1, 1) + r = dx**2 + dy**2 + dz**2 + r = dsqrt(r) + + ! normalized distance + dx = dx / r + dy = dy / r + dz = dz / r + + ! converting distance to Angstrom as the potential was done + r = r / ANG + + ! calculating diabatic hamiltonian + VX = (nai%a2 + (nai%b2 / r)**8) * dexp(-r / nai%rho) - nai%e2 / r - nai%e2 * (nai%lp + nai%lm) / 2 / r**4 - & + nai%c2 / r**6 - 2 * nai%e2 * nai%lm * nai%lp / r**7 + nai%de0 + VA = nai%a1 * dexp(-nai%beta1 * (r - nai%r0)) + VXA = nai%a12 * dexp(-nai%beta12 * (r - nai%rx)**2) + ! calculating derivatives of diabatic hamiltonian + dVX = -(nai%a2 + (nai%b2 / r)**8) * dexp(-r / nai%rho) / nai%rho - 8.0D0 * nai%b2**8 / r**9 * dexp(-r / nai%rho) + & + 14.0D0 * nai%e2 * nai%lm * nai%lp / r**8 + 6.0D0 * nai%c2 / r**7 + 2.0D0 * nai%e2 * (nai%lp + nai%lm) / r**5 + & + nai%e2 / r**2 + dVA = -nai%beta1 * VA + dVXA = -2.0D0 * nai%beta12 * (r - nai%rx) * VXA + ! converting them to a.u. as they are in eV or eV/Angstrom + VX = VX / AUTOEV + VA = VA / AUTOEV + VXA = VXA / AUTOEV + dVX = dVX / AUTOEV / ANG + dVA = dVA / AUTOEV / ANG + dVXA = dVXA / AUTOEV / ANG + + ! adiabatic potentials + E1 = (VA + VX) / 2.0D0 - dsqrt((VA - VX)**2.0D0 + 4.0D0 * VXA**2.0D0) / 2.0D0 + E2 = (VA + VX) / 2.0D0 + dsqrt((VA - VX)**2.0D0 + 4.0D0 * VXA**2.0D0) / 2.0D0 + ! nonadiabatic coupling vector in the reduced system + d12 = -(VXA * (dVA - dVX) + (-VA + VX) * dVXA) / (VA**2.0D0 - 2.0D0 * VA * VX + VX**2.0D0 + 4.0D0 * VXA**2.0D0) + d12 = d12 / ANG ! one more conversion necessary + ! derivatives of energies + dE1 = (dVA + dVX) / 2.0D0 - (2.0D0 * (VA - VX) * (dVA - dVX) + 8.0D0 * VXA * dVXA) / & + (4.0D0 * dsqrt((VA - VX)**2.0D0 + 4.0D0 * VXA**2.0D0)) + dE2 = (dVA + dVX) / 2.0D0 + (2.0D0 * (VA - VX) * (dVA - dVX) + 8.0D0 * VXA * dVXA) / & + (4.0D0 * dsqrt((VA - VX)**2.0D0 + 4.0D0 * VXA**2.0D0)) + + ! saving electronic energies for SH + en_array(1) = E1 + en_array(2) = E2 + + ! saving classical energy for Verlet + eclas = en_array(istate) + + ! calculate force (-dE/dr) on the propagated state + if (istate == 1) fr = -dE1 + if (istate == 2) fr = -dE2 + + ! projecting the force on the cartesian coordinates + fx(1, 1) = -fr * dx + fx(2, 1) = -fx(1, 1) + fy(1, 1) = -fr * dy + fy(2, 1) = -fy(1, 1) + fz(1, 1) = -fr * dz + fz(2, 1) = -fz(1, 1) + + ! projecting coupling to the cartesian coordinates + nacx(1, 1, 2) = -d12 * dx + nacy(1, 1, 2) = -d12 * dy + nacz(1, 1, 2) = -d12 * dz + nacx(1, 2, 1) = -nacx(1, 1, 2) + nacy(1, 2, 1) = -nacy(1, 1, 2) + nacz(1, 2, 1) = -nacz(1, 1, 2) + nacx(2, 1, 2) = d12 * dx + nacy(2, 1, 2) = d12 * dy + nacz(2, 1, 2) = d12 * dz + nacx(2, 2, 1) = -nacx(2, 1, 2) + nacy(2, 2, 1) = -nacy(2, 1, 2) + nacz(2, 2, 1) = -nacz(2, 1, 2) + + end subroutine force_nai + +end module mod_potentials_sh diff --git a/src/surfacehop.F90 b/src/surfacehop.F90 index 0ccc6d38..070411ee 100644 --- a/src/surfacehop.F90 +++ b/src/surfacehop.F90 @@ -287,6 +287,7 @@ subroutine get_nacm(pot) ! In TeraChem SH interface, we already got NACME if (pot == '_tera_') return + if (pot == '_nai_') return ! for NaI model, the couplings are calcualted together with forces ! Check whether we need to compute any NACME num_nacme = 0 @@ -611,16 +612,14 @@ subroutine surfacehop(x, y, z, vx, vy, vz, vx_old, vy_old, vz_old, dt, eclas) ! First, calculate NACME if (inac == 0) then - ! For TeraChem MPI / FMS interface, NAC are already computed! - if (pot /= '_tera_') then + if (pot /= '_tera_' .and. pot /= '_nai_') then nacx = 0.0D0 nacy = 0.0D0 nacz = 0.0D0 ! Compute and read NACME (MOLPRO-SH interface) call get_nacm(pot) end if - ! TODO: Should we call this with TeraChem? ! I think TC already phases the couplings internally. call phase_nacme(nacx_old, nacy_old, nacz_old, nacx, nacy, nacz) diff --git a/tests/SH_NaI/PES.dat.ref b/tests/SH_NaI/PES.dat.ref new file mode 100644 index 00000000..aec1e8d2 --- /dev/null +++ b/tests/SH_NaI/PES.dat.ref @@ -0,0 +1,6 @@ + # Time[fs] Potential energies + 0.06 -0.8731544800E-03 0.3904840511E-02 + 0.12 -0.8738840794E-03 0.3902676524E-02 + 0.18 -0.8746152732E-03 0.3900509975E-02 + 0.24 -0.8753480644E-03 0.3898340868E-02 + 0.30 -0.8760824558E-03 0.3896169203E-02 diff --git a/tests/SH_NaI/distances.dat.ref b/tests/SH_NaI/distances.dat.ref new file mode 100644 index 00000000..fadd3d9f --- /dev/null +++ b/tests/SH_NaI/distances.dat.ref @@ -0,0 +1,6 @@ + # Distances [Angstrom] + 0.06 7.2911701 + 0.12 7.2908894 + 0.18 7.2906084 + 0.24 7.2903270 + 0.30 7.2900452 diff --git a/tests/SH_NaI/dotprod.dat.ref b/tests/SH_NaI/dotprod.dat.ref new file mode 100644 index 00000000..19b0f4dc --- /dev/null +++ b/tests/SH_NaI/dotprod.dat.ref @@ -0,0 +1,6 @@ + # Time[fs] dotproduct(i,j) [i=1,nstate-1;j=i+1,nstate] + 0.06 -0.5679102843E-04 + 0.12 -0.5690157880E-04 + 0.18 -0.5701226238E-04 + 0.24 -0.5712307933E-04 + 0.30 -0.5723402981E-04 diff --git a/tests/SH_NaI/input.in b/tests/SH_NaI/input.in new file mode 100644 index 00000000..f9505055 --- /dev/null +++ b/tests/SH_NaI/input.in @@ -0,0 +1,37 @@ +This is a sample input file for Surface-Hopping simulation in ABIN + +&general +pot='_nai_' ! where do we obtain forces? +irest=0, ! should we restart from restart.xyz? +irandom=347110445, ! random seed + +mdtype='sh', ! sh = Surface Hopping non adiabatic MD +nstep=5, ! number of steps, originally in QD 260000 +dt=2.5, ! timestep [au], originally in QD 0.25 + +nwrite=1, ! how often some output should be printed (energies, surface hopping probabilities etc.) +nwritex=1, ! how often to print coordinates? +nwritev=1, ! how often to print coordinates? +narchive=90000, ! how often to print coordinates? +nrest=200, ! how often to print restart files? +/ + +&nhcopt +inose=0, ! NVE ensemble (thermostat turned OFF) +!temp=0.00, ! Usually, you would read initial velocities from previous ground state sampling (-v option) +/ + +&sh +istate_init=2, ! initial electronic state (1 is ground state) +nstate=2, ! number of electronic states +deltaE=2.0, ! maximum energy difference (eV) between states for which we calculate NA coupling +PopThr=0.00001, ! minimum population of either state, for which we compute NA coupling +EnergyDifThr=0.01, ! maximum energy difference between two consecutive steps +EnergyDriftThr=0.01, ! maximum energy drift from initial total energy +/ + +&system +ndist=1, +dist1=1, +dist2=2, +/ diff --git a/tests/SH_NaI/mini.xyz b/tests/SH_NaI/mini.xyz new file mode 100644 index 00000000..30df9d1c --- /dev/null +++ b/tests/SH_NaI/mini.xyz @@ -0,0 +1,4 @@ + 2 +Time step: 2700 Sim. Time [au] 6750.00 +I -0.71520124E+00 0.00000000E+00 0.00000000E+00 +Na 0.65762491E+01 0.00000000E+00 0.00000000E+00 diff --git a/tests/SH_NaI/nacm_all.dat.ref b/tests/SH_NaI/nacm_all.dat.ref new file mode 100644 index 00000000..c9399c8d --- /dev/null +++ b/tests/SH_NaI/nacm_all.dat.ref @@ -0,0 +1,20 @@ + Time step: 1 + NACME between states: 1 2 + -0.2678921537E+00 -0.0000000000E+00 -0.0000000000E+00 + 0.2678921537E+00 0.0000000000E+00 0.0000000000E+00 + Time step: 2 + NACME between states: 1 2 + -0.2680501091E+00 -0.0000000000E+00 -0.0000000000E+00 + 0.2680501091E+00 0.0000000000E+00 0.0000000000E+00 + Time step: 3 + NACME between states: 1 2 + -0.2682083260E+00 -0.0000000000E+00 -0.0000000000E+00 + 0.2682083260E+00 0.0000000000E+00 0.0000000000E+00 + Time step: 4 + NACME between states: 1 2 + -0.2683668044E+00 -0.0000000000E+00 -0.0000000000E+00 + 0.2683668044E+00 0.0000000000E+00 0.0000000000E+00 + Time step: 5 + NACME between states: 1 2 + -0.2685255443E+00 -0.0000000000E+00 -0.0000000000E+00 + 0.2685255443E+00 0.0000000000E+00 0.0000000000E+00 diff --git a/tests/SH_NaI/pop.dat.ref b/tests/SH_NaI/pop.dat.ref new file mode 100644 index 00000000..d3b75d0e --- /dev/null +++ b/tests/SH_NaI/pop.dat.ref @@ -0,0 +1,6 @@ + # Time[fs] CurrentState Populations Sum-of-Populations + 0.06 2 0.00000 1.00000 0.9999999 + 0.12 2 0.00000 1.00000 0.9999999 + 0.18 2 0.00000 1.00000 0.9999999 + 0.24 2 0.00000 1.00000 0.9999999 + 0.30 2 0.00000 1.00000 0.9999999 diff --git a/tests/SH_NaI/prob.dat.ref b/tests/SH_NaI/prob.dat.ref new file mode 100644 index 00000000..b3e79fbb --- /dev/null +++ b/tests/SH_NaI/prob.dat.ref @@ -0,0 +1,6 @@ + # Time[fs] CurrentState Probabilities + 0.06 2 0.00000 0.00000 + 0.12 2 0.00000 0.00000 + 0.18 2 0.00000 0.00000 + 0.24 2 0.00000 0.00000 + 0.30 2 0.00000 0.00000 diff --git a/tests/SH_NaI/restart.xyz.ref b/tests/SH_NaI/restart.xyz.ref new file mode 100644 index 00000000..00b23ca6 --- /dev/null +++ b/tests/SH_NaI/restart.xyz.ref @@ -0,0 +1,1297 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4.1156809361745417E-001 + 6.6301397816010166E-001 + 8.1213407037767382E-001 + 3.2830447169701316E-001 + 6.0129230390843702E-001 + 6.9404951173510909E-001 + 3.8991100451811178E-001 + 2.9239643059963072E-002 + 8.9575454044384273E-001 + 8.2052104975963758E-001 + 2.4670272453971265E-001 + 2.1959395860314856E-001 + 1.9404960160844098E-001 + 9.9969511490773044E-001 + 6.3920521364160265E-003 diff --git a/tests/SH_NaI/velocities.in b/tests/SH_NaI/velocities.in new file mode 100644 index 00000000..a33a5a72 --- /dev/null +++ b/tests/SH_NaI/velocities.in @@ -0,0 +1,4 @@ + 2 +Initial condition: 1 from 100000 Wigner samples +I 0.0000324705 0.0000000000 0.0000000000 +Na -0.0001792382 0.0000000000 0.0000000000 diff --git a/tests/test.sh b/tests/test.sh index ce9ed2cc..c32efd0c 100755 --- a/tests/test.sh +++ b/tests/test.sh @@ -125,7 +125,7 @@ if [[ $TESTS = "all" ]];then folders=(INIT CMD NHC-GLOBAL SHAKE \ SH_EULER SH_RK4 SH_BUTCHER SH_RK4_PHASE \ SH_IGNORE SH_NACM_FAIL SH_S0S1 SH_ENERGY_DIFF SH_ENERGY_DRIFT \ - SH_BUTCHER_PHASE SH_SIMPLE_RESCALE SH_FRUSTRATED \ + SH_BUTCHER_PHASE SH_SIMPLE_RESCALE SH_FRUSTRATED SH_NaI\ LZ_SS LZ_ST LZ_ENE \ PIMD ABINITIO ABINITIO-FAIL MTS \ LANGEVIN QT QT2 PIGLE PIGLE2 GLE-CANONICAL \