Introduce modular version.

src/thermo.c

@@ -0,0 +1,132 @@
+/*
+ * =======================================================================================
+ *
+ *      Author:   Jan Eitzinger (je), jan.eitzinger@fau.de
+ *      Copyright (c) 2020 RRZE, University Erlangen-Nuremberg
+ *
+ *      Permission is hereby granted, free of charge, to any person obtaining a copy
+ *      of this software and associated documentation files (the "Software"), to deal
+ *      in the Software without restriction, including without limitation the rights
+ *      to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ *      copies of the Software, and to permit persons to whom the Software is
+ *      furnished to do so, subject to the following conditions:
+ *
+ *      The above copyright notice and this permission notice shall be included in all
+ *      copies or substantial portions of the Software.
+ *
+ *      THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ *      IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ *      FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ *      AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ *      LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ *      OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ *      SOFTWARE.
+ *
+ * =======================================================================================
+ */
+#include <stdlib.h>
+#include <stdio.h>
+#include <math.h>
+
+#include <thermo.h>
+
+static int *steparr;
+static double *tmparr;
+static double *engarr;
+static double *prsarr;
+static double mvv2e;
+static int dof_boltz;
+static double t_scale;
+static double p_scale;
+static double e_scale;
+static double t_act;
+static double p_act;
+static double e_act;
+static int mstat;
+
+void setupThermo(Parameter *param, int natoms)
+{
+    int maxstat = param->ntimes / param->nstat + 2;
+
+    steparr = (int*) malloc(maxstat * sizeof(int));
+    tmparr = (double*) malloc(maxstat * sizeof(double));
+    engarr = (double*) malloc(maxstat * sizeof(double));
+    prsarr = (double*) malloc(maxstat * sizeof(double));
+
+    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;
+
+    printf("step\ttemp\t\tpressure\n");
+}
+
+void computeThermo(int iflag, Parameter *param, Atom *atom)
+{
+    double t = 0.0, p;
+    double* vx = atom->vx;
+    double* vy = atom->vy;
+    double* 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 */
+    double vxtot = 0.0; double vytot = 0.0; double vztot = 0.0;
+    double* vx = atom->vx; double* vy = atom->vy; double* 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;
+    double 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;
+    double factor = sqrt(param->temp / t);
+
+    for(int i = 0; i < atom->Nlocal; i++) {
+        vx[i] *= factor;
+        vy[i] *= factor;
+        vz[i] *= factor;
+    }
+}