git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8210 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/fix_gravity.cpp

@@ -20,6 +20,9 @@
 #include "update.h"
 #include "domain.h"
 #include "respa.h"
+#include "modify.h"
+#include "input.h"
+#include "variable.h"
 #include "math_const.h"
 #include "error.h"
 
@@ -27,7 +30,8 @@ using namespace LAMMPS_NS;
 using namespace FixConst;
 using namespace MathConst;
 
-enum{CHUTE,SPHERICAL,GRADIENT,VECTOR};
+enum{CHUTE,SPHERICAL,VECTOR};
+enum{CONSTANT,EQUAL};
 
 /* ---------------------------------------------------------------------- */
 
@@ -36,64 +40,92 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
 {
   if (narg < 5) error->all(FLERR,"Illegal fix gravity command");
 
-  time_depend = 1;
   scalar_flag = 1;
   global_freq = 1;
   extscalar = 1;
 
-  magnitude = atof(arg[3]);
+  mstr = vstr = pstr = tstr = xstr = ystr = zstr = NULL;
+  mstyle = vstyle = pstyle = tstyle = xstyle = ystyle = zstyle = CONSTANT;
+
+  if (strstr(arg[3],"v_") == arg[3]) {
+    int n = strlen(&arg[3][2]) + 1;
+    mstr = new char[n];
+    strcpy(mstr,&arg[3][2]);
+    mstyle = EQUAL;
+  } else {
+    magnitude = atof(arg[3]);
+    mstyle = CONSTANT;
+  }
 
   if (strcmp(arg[4],"chute") == 0) {
     if (narg != 6) error->all(FLERR,"Illegal fix gravity command");
     style = CHUTE;
-    phi = 0.0;
+    if (strstr(arg[5],"v_") == arg[5]) {
-    theta = 180.0 - atof(arg[5]);
+      int n = strlen(&arg[5][2]) + 1;
+      vstr = new char[n];
+      strcpy(vstr,&arg[5][2]);
+      vstyle = EQUAL;
+    } else {
+      vert = atof(arg[5]);
+      vstyle = CONSTANT;
+    }
+
   } else if (strcmp(arg[4],"spherical") == 0) {
     if (narg != 7) error->all(FLERR,"Illegal fix gravity command");
     style = SPHERICAL;
-    phi = atof(arg[5]);
+    if (strstr(arg[5],"v_") == arg[5]) {
-    theta = atof(arg[6]);
+      int n = strlen(&arg[5][2]) + 1;
-  } else if (strcmp(arg[4],"gradient") == 0) {
+      pstr = new char[n];
-    if (narg != 9) error->all(FLERR,"Illegal fix gravity command");
+      strcpy(pstr,&arg[5][2]);
-    style = GRADIENT;
+      pstyle = EQUAL;
-    phi = atof(arg[5]);
+    } else {
-    theta = atof(arg[6]);
+      phi = atof(arg[5]);
-    phigrad = atof(arg[7]);
+      pstyle = CONSTANT;
-    thetagrad = atof(arg[8]);
+    }
+    if (strstr(arg[6],"v_") == arg[6]) {
+      int n = strlen(&arg[6][2]) + 1;
+      tstr = new char[n];
+      strcpy(tstr,&arg[6][2]);
+      tstyle = EQUAL;
+    } else {
+      theta = atof(arg[6]);
+      tstyle = CONSTANT;
+    }
+
   } else if (strcmp(arg[4],"vector") == 0) {
     if (narg != 8) error->all(FLERR,"Illegal fix gravity command");
     style = VECTOR;
-    xdir = atof(arg[5]);
+    if (strstr(arg[5],"v_") == arg[5]) {
-    ydir = atof(arg[6]);
+      int n = strlen(&arg[5][2]) + 1;
-    zdir = atof(arg[7]);
+      xstr = new char[n];
+      strcpy(xstr,&arg[5][2]);
+      xstyle = EQUAL;
+    } else {
+      xdir = atof(arg[5]);
+      xstyle = CONSTANT;
+    }
+    if (strstr(arg[6],"v_") == arg[6]) {
+      int n = strlen(&arg[6][2]) + 1;
+      ystr = new char[n];
+      strcpy(ystr,&arg[6][2]);
+      ystyle = EQUAL;
+    } else {
+      ydir = atof(arg[6]);
+      ystyle = CONSTANT;
+    }
+    if (strstr(arg[7],"v_") == arg[7]) {
+      int n = strlen(&arg[7][2]) + 1;
+      zstr = new char[n];
+      strcpy(zstr,&arg[7][2]);
+      zstyle = EQUAL;
+    } else {
+      zdir = atof(arg[7]);
+      zstyle = CONSTANT;
+    }
+
   } else error->all(FLERR,"Illegal fix gravity command");
 
   degree2rad = MY_PI/180.0;
-
-  if (style == CHUTE || style == SPHERICAL || style == GRADIENT) {
-    if (domain->dimension == 3) {
-      xgrav = sin(degree2rad * theta) * cos(degree2rad * phi);
-      ygrav = sin(degree2rad * theta) * sin(degree2rad * phi);
-      zgrav = cos(degree2rad * theta);
-    } else {
-      xgrav = sin(degree2rad * theta);
-      ygrav = cos(degree2rad * theta);
-      zgrav = 0.0;
-    }
-  } else if (style == VECTOR) {
-    if (domain->dimension == 3) {
-      double length = sqrt(xdir*xdir + ydir*ydir + zdir*zdir);
-      xgrav = xdir/length;
-      ygrav = ydir/length;
-      zgrav = zdir/length;
-    } else {
-      double length = sqrt(xdir*xdir + ydir*ydir);
-      xgrav = xdir/length;
-      ygrav = ydir/length;
-      zgrav = 0.0;
-    }
-  }
-
   time_origin = update->ntimestep;
 
   eflag = 0;
@@ -102,6 +134,19 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
 
 /* ---------------------------------------------------------------------- */
 
+FixGravity::~FixGravity()
+{
+  delete [] mstr;
+  delete [] vstr;
+  delete [] pstr;
+  delete [] tstr;
+  delete [] xstr;
+  delete [] ystr;
+  delete [] zstr;
+}
+
+/* ---------------------------------------------------------------------- */
+
 int FixGravity::setmask()
 {
   int mask = 0;
@@ -118,11 +163,66 @@ void FixGravity::init()
   if (strstr(update->integrate_style,"respa"))
     nlevels_respa = ((Respa *) update->integrate)->nlevels;
 
-  dt = update->dt;
+  // check variables
 
-  xacc = magnitude*xgrav;
+  if (mstr) {
-  yacc = magnitude*ygrav;
+    mvar = input->variable->find(mstr);
-  zacc = magnitude*zgrav;
+    if (mvar < 0) 
+      error->all(FLERR,"Variable name for fix gravity does not exist");
+    if (!input->variable->equalstyle(mvar))
+      error->all(FLERR,"Variable for fix gravity is invalid style");
+  }
+  if (vstr) {
+    vvar = input->variable->find(vstr);
+    if (vvar < 0) 
+      error->all(FLERR,"Variable name for fix gravity does not exist");
+    if (!input->variable->equalstyle(vvar))
+      error->all(FLERR,"Variable for fix gravity is invalid style");
+  }
+  if (pstr) {
+    pvar = input->variable->find(pstr);
+    if (pvar < 0) 
+      error->all(FLERR,"Variable name for fix gravity does not exist");
+    if (!input->variable->equalstyle(pvar))
+      error->all(FLERR,"Variable for fix gravity is invalid style");
+  }
+  if (tstr) {
+    tvar = input->variable->find(tstr);
+    if (tvar < 0) 
+      error->all(FLERR,"Variable name for fix gravity does not exist");
+    if (!input->variable->equalstyle(tvar))
+      error->all(FLERR,"Variable for fix gravity is invalid style");
+  }
+  if (xstr) {
+    xvar = input->variable->find(xstr);
+    if (xvar < 0) 
+      error->all(FLERR,"Variable name for fix gravity does not exist");
+    if (!input->variable->equalstyle(xvar))
+      error->all(FLERR,"Variable for fix gravity is invalid style");
+  }
+  if (ystr) {
+    yvar = input->variable->find(ystr);
+    if (yvar < 0) 
+      error->all(FLERR,"Variable name for fix gravity does not exist");
+    if (!input->variable->equalstyle(yvar))
+      error->all(FLERR,"Variable for fix gravity is invalid style");
+  }
+  if (zstr) {
+    zvar = input->variable->find(zstr);
+    if (zvar < 0) 
+      error->all(FLERR,"Variable name for fix gravity does not exist");
+    if (!input->variable->equalstyle(zvar))
+      error->all(FLERR,"Variable for fix gravity is invalid style");
+  }
+
+  varflag = CONSTANT;
+  if (mstyle != CONSTANT || vstyle != CONSTANT || pstyle != CONSTANT || 
+      tstyle != CONSTANT || xstyle != CONSTANT || ystyle != CONSTANT || 
+      zstyle != CONSTANT) varflag = EQUAL;
+
+  // set gravity components once and for all
+
+  if (varflag == CONSTANT) set_acceleration();
 }
 
 /* ---------------------------------------------------------------------- */
@@ -142,26 +242,20 @@ void FixGravity::setup(int vflag)
 
 void FixGravity::post_force(int vflag)
 {
-  // update direction of gravity vector if gradient style
+  // update gravity due to variables
 
-  if (style == GRADIENT) {
+  if (varflag != CONSTANT) {
-    if (domain->dimension == 3) {
+    modify->clearstep_compute();
-      double phi_current = degree2rad * 
+    if (mstyle == EQUAL) magnitude = input->variable->compute_equal(mvar);
-	(phi + (update->ntimestep - time_origin)*dt*phigrad*360.0);
+    if (vstyle == EQUAL) magnitude = input->variable->compute_equal(vvar);
-      double theta_current = degree2rad * 
+    if (pstyle == EQUAL) magnitude = input->variable->compute_equal(pvar);
-	(theta + (update->ntimestep - time_origin)*dt*thetagrad*360.0);
+    if (tstyle == EQUAL) magnitude = input->variable->compute_equal(tvar);
-      xgrav = sin(theta_current) * cos(phi_current);
+    if (xstyle == EQUAL) magnitude = input->variable->compute_equal(xvar);
-      ygrav = sin(theta_current) * sin(phi_current);
+    if (ystyle == EQUAL) magnitude = input->variable->compute_equal(yvar);
-      zgrav = cos(theta_current);
+    if (zstyle == EQUAL) magnitude = input->variable->compute_equal(zvar);
-    } else {
+    modify->addstep_compute(update->ntimestep + 1);
-      double theta_current = degree2rad * 
+
-	(theta + (update->ntimestep - time_origin)*dt*thetagrad*360.0);
+    set_acceleration();
-      xgrav = sin(theta_current);
-      ygrav = cos(theta_current);
-    }
-    xacc = magnitude*xgrav;
-    yacc = magnitude*ygrav;
-    zacc = magnitude*zgrav;
   }
 
   double **x = atom->x;
@@ -204,6 +298,43 @@ void FixGravity::post_force_respa(int vflag, int ilevel, int iloop)
   if (ilevel == nlevels_respa-1) post_force(vflag);
 }
 
+/* ---------------------------------------------------------------------- */
+
+void FixGravity::set_acceleration()
+{
+  if (style == CHUTE || style == SPHERICAL) {
+    if (style == CHUTE) {
+      phi = 0.0;
+      theta = 180.0 - vert;
+    }
+    if (domain->dimension == 3) {
+      xgrav = sin(degree2rad * theta) * cos(degree2rad * phi);
+      ygrav = sin(degree2rad * theta) * sin(degree2rad * phi);
+      zgrav = cos(degree2rad * theta);
+    } else {
+      xgrav = sin(degree2rad * theta);
+      ygrav = cos(degree2rad * theta);
+      zgrav = 0.0;
+    }
+  } else if (style == VECTOR) {
+    if (domain->dimension == 3) {
+      double length = sqrt(xdir*xdir + ydir*ydir + zdir*zdir);
+      xgrav = xdir/length;
+      ygrav = ydir/length;
+      zgrav = zdir/length;
+    } else {
+      double length = sqrt(xdir*xdir + ydir*ydir);
+      xgrav = xdir/length;
+      ygrav = ydir/length;
+      zgrav = 0.0;
+    }
+  }
+
+  xacc = magnitude*xgrav;
+  yacc = magnitude*ygrav;
+  zacc = magnitude*zgrav;
+}
+
 /* ----------------------------------------------------------------------
    potential energy in gravity field
 ------------------------------------------------------------------------- */

src/fix_gravity.h

@@ -29,6 +29,7 @@ class FixGravity : public Fix {
 
  public:
   FixGravity(class LAMMPS *, int, char **);
+  ~FixGravity();
   int setmask();
   void init();
   void setup(int);
@@ -38,8 +39,8 @@ class FixGravity : public Fix {
 
  protected:
   int style;
-  double magnitude,dt;
+  double magnitude;
-  double phi,theta,phigrad,thetagrad;
+  double vert,phi,theta;
   double xdir,ydir,zdir;
   double xgrav,ygrav,zgrav,xacc,yacc,zacc;
   double degree2rad;
@@ -47,6 +48,13 @@ class FixGravity : public Fix {
   int time_origin;
   int eflag;
   double egrav,egrav_all;
+
+  int varflag;
+  int mstyle,vstyle,pstyle,tstyle,xstyle,ystyle,zstyle;
+  int mvar,vvar,pvar,tvar,xvar,yvar,zvar;
+  char *mstr,*vstr,*pstr,*tstr,*xstr,*ystr,*zstr;
+
+  void set_acceleration();
 };
 
 }

src/fix_move.cpp

@@ -50,7 +50,6 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
   size_peratom_cols = 3;
   peratom_freq = 1;
   time_integrate = 1;
-  time_depend = 1;
   create_attribute = 1;
 
   // parse args
@@ -177,9 +176,11 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
     if (mstyle == WIGGLE && azflag && az != 0.0)
       error->all(FLERR,"Fix move cannot set wiggle z motion for 2d problem");
     if (mstyle == ROTATE && (axis[0] != 0.0 || axis[1] != 0.0))
-      error->all(FLERR,"Fix move cannot rotate aroung non z-axis for 2d problem");
+      error->all(FLERR,
+		 "Fix move cannot rotate aroung non z-axis for 2d problem");
     if (mstyle == VARIABLE && (zvarstr || vzvarstr))
-      error->all(FLERR,"Fix move cannot define z or vz variable for 2d problem");
+      error->all(FLERR,
+		 "Fix move cannot define z or vz variable for 2d problem");
   }
 
   if (atom->angmom_flag && comm->me == 0)
@@ -310,42 +311,48 @@ void FixMove::init()
   if (mstyle == VARIABLE) {
     if (xvarstr) {
       xvar = input->variable->find(xvarstr);
-      if (xvar < 0) error->all(FLERR,"Variable name for fix move does not exist");
+      if (xvar < 0) error->all(FLERR,
+			       "Variable name for fix move does not exist");
       if (input->variable->equalstyle(xvar)) xvarstyle = EQUAL;
       else if (input->variable->atomstyle(xvar)) xvarstyle = ATOM;
       else error->all(FLERR,"Variable for fix move is invalid style");
     }
     if (yvarstr) {
       yvar = input->variable->find(yvarstr);
-      if (yvar < 0) error->all(FLERR,"Variable name for fix move does not exist");
+      if (yvar < 0) error->all(FLERR,
+			       "Variable name for fix move does not exist");
       if (input->variable->equalstyle(yvar)) yvarstyle = EQUAL;
       else if (input->variable->atomstyle(yvar)) yvarstyle = ATOM;
       else error->all(FLERR,"Variable for fix move is invalid style");
     }
     if (zvarstr) {
       zvar = input->variable->find(zvarstr);
-      if (zvar < 0) error->all(FLERR,"Variable name for fix move does not exist");
+      if (zvar < 0) error->all(FLERR,
+			       "Variable name for fix move does not exist");
       if (input->variable->equalstyle(zvar)) zvarstyle = EQUAL;
       else if (input->variable->atomstyle(zvar)) zvarstyle = ATOM;
       else error->all(FLERR,"Variable for fix move is invalid style");
     }
     if (vxvarstr) {
       vxvar = input->variable->find(vxvarstr);
-      if (vxvar < 0) error->all(FLERR,"Variable name for fix move does not exist");
+      if (vxvar < 0) error->all(FLERR,
+				"Variable name for fix move does not exist");
       if (input->variable->equalstyle(vxvar)) vxvarstyle = EQUAL;
       else if (input->variable->atomstyle(vxvar)) vxvarstyle = ATOM;
       else error->all(FLERR,"Variable for fix move is invalid style");
     }
     if (vyvarstr) {
       vyvar = input->variable->find(vyvarstr);
-      if (vyvar < 0) error->all(FLERR,"Variable name for fix move does not exist");
+      if (vyvar < 0) error->all(FLERR,
+				"Variable name for fix move does not exist");
       if (input->variable->equalstyle(vyvar)) vyvarstyle = EQUAL;
       else if (input->variable->atomstyle(vyvar)) vyvarstyle = ATOM;
       else error->all(FLERR,"Variable for fix move is invalid style");
     }
     if (vzvarstr) {
       vzvar = input->variable->find(vzvarstr);
-      if (vzvar < 0) error->all(FLERR,"Variable name for fix move does not exist");
+      if (vzvar < 0) error->all(FLERR,
+				"Variable name for fix move does not exist");
       if (input->variable->equalstyle(vzvar)) vzvarstyle = EQUAL;
       else if (input->variable->atomstyle(vzvar)) vzvarstyle = ATOM;
       else error->all(FLERR,"Variable for fix move is invalid style");

src/read_dump.cpp

@@ -15,6 +15,7 @@
    Contributing author: Timothy Sirk (U Vermont)
 ------------------------------------------------------------------------- */
 
+#include "lmptype.h"
 #include "mpi.h"
 #include "string.h"
 #include "stdlib.h"