Re: [AMBER] REMD with pressure coupling

From: Neale, Christopher Andrew <cneale.lanl.gov> Date: Tue, 20 Dec 2016 17:09:43 +0000

---
> !    if (ntp .gt. 0) then
> !
> !      write(mdout, '(a,a)') error_hdr, 'REMD cannot be run with ntp > 0!'
> !      inerr = 1
> !
> !    end if
$ diff amber16/src/pmemd/src/runmd.F90 amber16_pressremdPROPER/src/pmemd/src/runmd.F90 
895c895,896
<                                     si(si_kin_ene) / fac(1), print_exch_data, &
---
>                                     si(si_kin_ene) / fac(1), pres0, &
>                                     si(si_volume), print_exch_data, &
$ diff amber16/src/pmemd/src/remd_exchg.F90 amber16_pressremdPROPER/src/pmemd/src/remd_exchg.F90 
68c68,69
<   use pmemd_lib_mod, only   : strip
---
>   use pmemd_lib_mod, only   : strip,mexit
> 
158,159c159,162
<       call temperature_exchange(atm_cnt, vel, remd_ptot, my_dim, remd_size, &
<                                 actual_temperature, .true., mdloop)
---
>       write(mdout, '(/,a)') ' PV for 2D-REMD not implemented. Exiting.'
>       call mexit(mdout, 1)
>       !call temperature_exchange(atm_cnt, vel, remd_ptot, my_dim, remd_size, &
>       !                          actual_temperature, .true., mdloop)
314a318
>                                 actual_pressure, actual_volume, &
330a335,336
>   double precision, intent(in)    :: actual_pressure
>   double precision, intent(in)    :: actual_volume
340a347,348
>     double precision :: real_pres
>     double precision :: real_vol
347c355
<   integer, parameter :: SIZE_EXCHANGE_DATA = 6 ! for mpi_gather
---
>   integer, parameter :: SIZE_EXCHANGE_DATA = 8 ! for mpi_gather
354a363
>   double precision  :: pressurevolumedelta
392a402,403
>   my_exch_data%real_pres   = actual_pressure
>   my_exch_data%real_vol    = actual_volume
460a472,480
>       ! * 0.0602214 / 4184 converts units to kcal/mol
>       pressurevolumedelta = &
>         (((ONEKB / my_exch_data%temp0) * &
>           my_exch_data%real_pres) - &
>          ((ONEKB / exch_data_tbl(neighbor_rank+1)%temp0) * &
>             exch_data_tbl(neighbor_rank+1)%real_pres)) * &
>          (my_exch_data%real_vol - exch_data_tbl(neighbor_rank+1)%real_vol) * &
>         0.0602214 / 4184.0
> 
465c485,486
<               (my_exch_data%temp0 * exch_data_tbl(neighbor_rank+1)%temp0)
---
>               (my_exch_data%temp0 * exch_data_tbl(neighbor_rank+1)%temp0) &
>               - pressurevolumedelta
485,487c506,515
<       write(mdout,'(a8,E16.6,a8,E16.6,a12,f10.2)') &
<                "Metrop= ",metrop," delta= ",delta," o_scaling= ", &
<                1 / my_exch_data%scaling
---
>       write(mdout,'(a8,E16.6,a8,E16.6,a8,E16.6,a5,E16.6,a5,E16.6,a5,E16.6,a5,E16.6,a5,E16.6,a5,E16.6,a12,f10.2)') &
>                "Metrop= ",metrop," delta= ",delta, &
>                " pvwrk= ", pressurevolumedelta, &
>                " T1= ", my_exch_data%temp0, &
>                " T2= ", exch_data_tbl(neighbor_rank+1)%temp0, &
>                " P1= ", my_exch_data%real_pres, &
>                " P2= ", exch_data_tbl(neighbor_rank+1)%real_pres, &
>                " V1= ", my_exch_data%real_vol, &
>                " V2= ", exch_data_tbl(neighbor_rank+1)%real_vol, &
>                " o_scaling= ", 1 / my_exch_data%scaling
$ diff amber16/src/pmemd/src/cuda/gpu.cpp amber16_pressremdPROPER/src/pmemd/src/cuda/gpu.cpp
6306,6325c6306,6325
<     if (skin <= 0.5)
<     {
<         printf("ERROR: Calculation halted.");
<         printf("  Periodic box dimensions have changed too much from their initial values.\n");
<         printf("  Your system density has likely changed by a large amount, probably from\n");
<         printf("  starting the simulation from a structure a long way from equilibrium.\n");
<         printf("\n"); 
<         printf("  [Although this error can also occur if the simulation has blown up for some reason]\n");
<         printf("\n");
<         printf("  The GPU code does not automatically reorganize grid cells and thus you\n");
<         printf("  will need to restart the calculation from the previous restart file.\n");
<         printf("  This will generate new grid cells and allow the calculation to continue.\n");
<         printf("  It may be necessary to repeat this restarting multiple times if your system\n");
<         printf("  is a long way from an equilibrated density.\n");
<         printf("\n");
<         printf("  Alternatively you can run with the CPU code until the density has converged\n");
<         printf("  and then switch back to the GPU code.\n");
<         printf("\n");
<         exit(-1);
<     }
---
> //    if (skin <= 0.5)
> //    {
> //        printf("ERROR: Calculation halted.");
> //        printf("  Periodic box dimensions have changed too much from their initial values.\n");
> //        printf("  Your system density has likely changed by a large amount, probably from\n");
> //        printf("  starting the simulation from a structure a long way from equilibrium.\n");
> //        printf("\n"); 
> //        printf("  [Although this error can also occur if the simulation has blown up for some reason]\n");
> //        printf("\n");
> //        printf("  The GPU code does not automatically reorganize grid cells and thus you\n");
> //        printf("  will need to restart the calculation from the previous restart file.\n");
> //        printf("  This will generate new grid cells and allow the calculation to continue.\n");
> //        printf("  It may be necessary to repeat this restarting multiple times if your system\n");
> //        printf("  is a long way from an equilibrated density.\n");
> //        printf("\n");
> //        printf("  Alternatively you can run with the CPU code until the density has converged\n");
> //        printf("  and then switch back to the GPU code.\n");
> //        printf("\n");
> //        exit(-1);
> //    }
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