!*********************************************************************** ! This program is part of the ! OpenMP Source Code Repository ! ! http://www.pcg.ull.es/ompscr/ ! e-mail: ompbench@etsii.ull.es ! ! This program is free software; you can redistribute it and/or modify ! it under the terms of the GNU General Public License as published by ! the Free Software Foundation; either version 2 of the License, or ! (at your option) any later version. ! ! This program is distributed in the hope that it will be useful, ! but WITHOUT ANY WARRANTY; without even the implied warranty of ! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ! GNU General Public License for more details. ! ! You should have received a copy of the GNU General Public License ! (LICENSE file) along with this program; if not, write to ! the Free Software Foundation, Inc., 59 Temple Place, Suite 330, ! Boston, MA 02111-1307 USA ! ! ! FILE: f_md.f90 ! VERSION: 1.0 ! DATE: May 2004 ! AUTHOR: Bill Magro, Kuck and Associates, Inc. (KAI), 1998 ! COMMENTS TO: sande@csi.ull.es ! DESCRIPTION: This program implements a simple molecular dynamics simulation, ! using the velocity Verlet time integration scheme. ! The particles interact with a central pair potential. ! COMMENTS: ! REFERENCES: W. C. Swope and H. C. Andersen and P. H. Berens and K. R. Wilson ! A Computer Simulation Method for the Calculation of ! Equilibrium Constants for the Formation of Physical ! Clusters of Molecues: Application to Small Water Clusters ! Journal of Chemical Physics, 1982 vol. 76 pg 637-649 ! BASIC PRAGMAS: parallel do ! USAGE: ./f_md.par 4096 10 ! INPUT: Number of particles ! Number of simulation steps ! OUTPUT: - ! FILE FORMATS: - ! RESTRICTIONS: An excessive number of particles might cause a runtime error ! in the parallel application if memory is not enough. ! REVISION HISTORY: !************************************************************************** program md_fortran USE oscrCommon_f USE omp_lib implicit none ! simulation parameters integer ndim ! dimensionality of the physical space integer NPARTS_DEF ! number of particles integer NPARTS_MAX ! number of particles integer NSTEPS_DEF ! number of time steps in the simulation parameter(ndim=3,NPARTS_DEF=4096,NPARTS_MAX=100000,NSTEPS_DEF=10) integer, parameter :: NUM_ARGS = 2 integer, parameter :: NUM_TIMERS = 1 real*8 mass ! mass of the particles real*8 dt ! time step real*8 box(ndim) ! dimensions of the simulation box parameter(mass=1.0,dt=1.0e-4) ! simulation variables integer nparts ! number of particles integer nsteps ! number of time steps in the simulation real*8 position(ndim,NPARTS_MAX) real*8 velocity(ndim,NPARTS_MAX) real*8 force(ndim,NPARTS_MAX) real*8 accel(ndim,NPARTS_MAX) real*8 potential, kinetic, E0 integer i integer :: NUMTHREADS character(len=8),dimension(NUM_ARGS) :: argNames = (/ 'NPARTS', 'NSTEPS' /) character(len=8),dimension(NUM_ARGS) :: defaultValues = (/ '4096', ' 10' /) character(len=8),dimension(NUM_TIMERS) :: timerNames = (/ 'EXE_TIME' /) double precision :: total_time box(1:ndim) = 10. NUMTHREADS = omp_get_max_threads() call OSCR_init( NUMTHREADS, & "Molecular dynamic simulation", & '', & NUM_ARGS, & argNames, & defaultValues, & NUM_TIMERS, & NUM_TIMERS, & timerNames ) nparts = OSCR_getarg_integer(1) nsteps = OSCR_getarg_integer(2) ! set initial positions, velocities, and accelerations call initialize(nparts,ndim,box,position,velocity,accel) call OSCR_timer_start(NUM_TIMERS) ! compute the forces and energies call compute(nparts,ndim,box,position,velocity,mass,force,potential,kinetic) E0 = potential + kinetic ! This is the main time stepping loop do i=1,nsteps call compute(nparts,ndim,box,position,velocity,mass, force,potential,kinetic) ! write(*,*) potential, kinetic,(potential + kinetic - E0)/E0 call update(nparts,ndim,position,velocity,force,accel,mass,dt) enddo call OSCR_timer_stop(NUM_TIMERS) total_time = OSCR_timer_read(NUM_TIMERS) call OSCR_report() end !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! Compute the forces and energies, given positions, masses, ! and velocities !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! subroutine compute(np,nd,box,pos,vel,mass,f,pot,kin) implicit none integer np integer nd real*8 box(nd) real*8 pos(nd,np) real*8 vel(nd,np) real*8 f(nd,np) real*8 mass real*8 pot real*8 kin real*8 dotr8 external dotr8 real*8 v, dv, x integer i, j, k real*8 rij(nd) real*8 d real*8 PI2 parameter(PI2=3.14159265d0/2.0d0) ! statement function for the pair potential and its derivative ! This potential is a harmonic well which smoothly saturates to a ! maximum value at PI/2. v(x) = sin(min(x,PI2))**2. dv(x) = 2.*sin(min(x,PI2))*cos(min(x,PI2)) pot = 0.0 kin = 0.0 ! The computation of forces and energies is fully parallel. !$OMP PARALLEL DO DEFAULT(SHARED) PRIVATE(i,j,k,rij,d) & !$OMP REDUCTION(+ : pot, kin) do i=1,np ! compute potential energy and forces f(1:nd,i) = 0.0 do j=1,np if (i .ne. j) then call dist(nd,box,pos(1,i),pos(1,j),rij,d) ! attribute half of the potential energy to particle 'j' pot = pot + 0.5*v(d) do k=1,nd f(k,i) = f(k,i) - rij(k)*dv(d)/d enddo endif enddo ! compute kinetic energy kin = kin + dotr8(nd,vel(1,i),vel(1,i)) enddo !$omp end parallel do kin = kin*0.5*mass return end !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! Initialize the positions, velocities, and accelerations. ! The Fortran90 random_number function is used to choose positions. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! subroutine initialize(np,nd,box,pos,vel,acc) implicit none integer np integer nd real*8 box(nd) real*8 pos(nd,np) real*8 vel(nd,np) real*8 acc(nd,np) integer i, j real*8 x do i=1,np do j=1,nd call random_number(x) pos(j,i) = box(j)*x vel(j,i) = 0.0 acc(j,i) = 0.0 enddo enddo return end ! Compute the displacement vector (and its norm) between two particles. subroutine dist(nd,box,r1,r2,dr,d) implicit none integer nd real*8 box(nd) real*8 r1(nd) real*8 r2(nd) real*8 dr(nd) real*8 d integer i d = 0.0 do i=1,nd dr(i) = r1(i) - r2(i) d = d + dr(i)**2. enddo d = sqrt(d) return end ! Return the dot product between two vectors of type real*8 and length n real*8 function dotr8(n,x,y) implicit none integer n real*8 x(n) real*8 y(n) integer i dotr8 = 0.0 do i = 1,n dotr8 = dotr8 + x(i)*y(i) enddo return end !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! Perform the time integration, using a velocity Verlet algorithm !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! subroutine update(np,nd,pos,vel,f,a,mass,dt) implicit none integer np integer nd real*8 pos(nd,np) real*8 vel(nd,np) real*8 f(nd,np) real*8 a(nd,np) real*8 mass real*8 dt integer i, j real*8 rmass rmass = 1.0/mass ! The time integration is fully parallel !$omp parallel do & !$omp default(shared) & !$omp private(i,j) do i = 1,np do j = 1,nd pos(j,i) = pos(j,i) + vel(j,i)*dt + 0.5*dt*dt*a(j,i) vel(j,i) = vel(j,i) + 0.5*dt*(f(j,i)*rmass + a(j,i)) a(j,i) = f(j,i)*rmass enddo enddo !$omp end parallel do return end