Rename default directory to lammps and reorganize gromacs variant steps

Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-01-25 21:00:11 +01:00
parent cbe42b8149
commit aa0f4048d0
34 changed files with 12 additions and 9 deletions
--- a/lammps/thermo.c
+++ b/lammps/thermo.c
@@ -0,0 +1,138 @@
+/*
+ * =======================================================================================
+ *
+ *   Author:   Jan Eitzinger (je), jan.eitzinger@fau.de
+ *   Copyright (c) 2020 RRZE, University Erlangen-Nuremberg
+ *
+ *   This file is part of MD-Bench.
+ *
+ *   MD-Bench is free software: you can redistribute it and/or modify it
+ *   under the terms of the GNU Lesser General Public License as published
+ *   by the Free Software Foundation, either version 3 of the License, or
+ *   (at your option) any later version.
+ *
+ *   MD-Bench 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 Lesser General Public License for more
+ *   details.
+ *
+ *   You should have received a copy of the GNU Lesser General Public License along
+ *   with MD-Bench.  If not, see <https://www.gnu.org/licenses/>.
+ * =======================================================================================
+ */
+#include <stdlib.h>
+#include <stdio.h>
+#include <math.h>
+
+#include <thermo.h>
+#include <util.h>
+
+static int *steparr;
+static MD_FLOAT *tmparr;
+static MD_FLOAT *engarr;
+static MD_FLOAT *prsarr;
+static MD_FLOAT mvv2e;
+static MD_FLOAT dof_boltz;
+static MD_FLOAT t_scale;
+static MD_FLOAT p_scale;
+static MD_FLOAT e_scale;
+static MD_FLOAT t_act;
+static MD_FLOAT p_act;
+static MD_FLOAT e_act;
+static int mstat;
+
+/* exported subroutines */
+void setupThermo(Parameter *param, int natoms)
+{
+    int maxstat = param->ntimes / param->nstat + 2;
+
+    steparr = (int*) malloc(maxstat * sizeof(int));
+    tmparr = (MD_FLOAT*) malloc(maxstat * sizeof(MD_FLOAT));
+    engarr = (MD_FLOAT*) malloc(maxstat * sizeof(MD_FLOAT));
+    prsarr = (MD_FLOAT*) malloc(maxstat * sizeof(MD_FLOAT));
+
+    if(param->force_field == FF_LJ) {
+        mvv2e = 1.0;
+        dof_boltz = (natoms * 3 - 3);
+        t_scale = mvv2e / dof_boltz;
+        p_scale = 1.0 / 3 / param->xprd / param->yprd / param->zprd;
+        e_scale = 0.5;
+    } else {
+        mvv2e = 1.036427e-04;
+        dof_boltz = (natoms * 3 - 3) * 8.617343e-05;
+        t_scale = mvv2e / dof_boltz;
+        p_scale = 1.602176e+06 / 3 / param->xprd / param->yprd / param->zprd;
+        e_scale = 524287.985533;//16.0;
+        param->dtforce /= mvv2e;
+    }
+
+    printf("step\ttemp\t\tpressure\n");
+}
+
+void computeThermo(int iflag, Parameter *param, Atom *atom)
+{
+    MD_FLOAT t = 0.0, p;
+    MD_FLOAT* vx = atom->vx;
+    MD_FLOAT* vy = atom->vy;
+    MD_FLOAT* vz = atom->vz;
+
+    for(int i = 0; i < atom->Nlocal; i++) {
+        t += (vx[i] * vx[i] + vy[i] * vy[i] + vz[i] * vz[i]) * param->mass;
+    }
+
+    t = t * t_scale;
+    p = (t * dof_boltz) * p_scale;
+    int istep = iflag;
+
+    if(iflag == -1){
+        istep = param->ntimes;
+    }
+    if(iflag == 0){
+        mstat = 0;
+    }
+
+    steparr[mstat] = istep;
+    tmparr[mstat] = t;
+    prsarr[mstat] = p;
+    mstat++;
+    fprintf(stdout, "%i\t%e\t%e\n", istep, t, p);
+}
+
+void adjustThermo(Parameter *param, Atom *atom)
+{
+    /* zero center-of-mass motion */
+    MD_FLOAT vxtot = 0.0; MD_FLOAT vytot = 0.0; MD_FLOAT vztot = 0.0;
+    MD_FLOAT* vx = atom->vx; MD_FLOAT* vy = atom->vy; MD_FLOAT* vz = atom->vz;
+
+    for(int i = 0; i < atom->Nlocal; i++) {
+        vxtot += vx[i];
+        vytot += vy[i];
+        vztot += vz[i];
+    }
+
+    vxtot = vxtot / atom->Natoms;
+    vytot = vytot / atom->Natoms;
+    vztot = vztot / atom->Natoms;
+
+    for(int i = 0; i < atom->Nlocal; i++) {
+        vx[i] -= vxtot;
+        vy[i] -= vytot;
+        vz[i] -= vztot;
+    }
+
+    t_act = 0;
+    MD_FLOAT t = 0.0;
+
+    for(int i = 0; i < atom->Nlocal; i++) {
+        t += (vx[i] * vx[i] + vy[i] * vy[i] + vz[i] * vz[i]) * param->mass;
+    }
+
+    t *= t_scale;
+    MD_FLOAT factor = sqrt(param->temp / t);
+
+    for(int i = 0; i < atom->Nlocal; i++) {
+        vx[i] *= factor;
+        vy[i] *= factor;
+        vz[i] *= factor;
+    }
+}