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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7003 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2011-09-23 18:06:55 +00:00
parent 2d99de131d
commit 19e8c92a90
468 changed files with 4628 additions and 5204 deletions
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50
src/fix_shake.cpp
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@ -37,8 +37,6 @@ using namespace LAMMPS_NS;
#define BIG 1.0e20
#define MASSDELTA 0.1
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
@ -56,7 +54,7 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
// error check
if (atom->molecular == 0)
error->all("Cannot use fix shake with non-molecular system");
error->all(FLERR,"Cannot use fix shake with non-molecular system");
// perform initial allocation of atom-based arrays
// register with Atom class
@ -74,7 +72,7 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
// parse SHAKE args
if (narg < 8) error->all("Illegal fix shake command");
if (narg < 8) error->all(FLERR,"Illegal fix shake command");
tolerance = atof(arg[3]);
max_iter = atoi(arg[4]);
@ -109,28 +107,28 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
} else if (mode == 'b') {
int i = atoi(arg[next]);
if (i < 1 || i > atom->nbondtypes)
error->all("Invalid bond type index for fix shake");
error->all(FLERR,"Invalid bond type index for fix shake");
bond_flag[i] = 1;
} else if (mode == 'a') {
int i = atoi(arg[next]);
if (i < 1 || i > atom->nangletypes)
error->all("Invalid angle type index for fix shake");
error->all(FLERR,"Invalid angle type index for fix shake");
angle_flag[i] = 1;
} else if (mode == 't') {
int i = atoi(arg[next]);
if (i < 1 || i > atom->ntypes)
error->all("Invalid atom type index for fix shake");
error->all(FLERR,"Invalid atom type index for fix shake");
type_flag[i] = 1;
} else if (mode == 'm') {
double massone = atof(arg[next]);
if (massone == 0.0) error->all("Invalid atom mass for fix shake");
if (nmass == atom->ntypes) error->all("Too many masses for fix shake");
if (massone == 0.0) error->all(FLERR,"Invalid atom mass for fix shake");
if (nmass == atom->ntypes) error->all(FLERR,"Too many masses for fix shake");
mass_list[nmass++] = massone;
} else error->all("Illegal fix shake command");
} else error->all(FLERR,"Illegal fix shake command");
next++;
}
@ -280,13 +278,13 @@ void FixShake::init()
int count = 0;
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"shake") == 0) count++;
if (count > 1) error->all("More than one fix shake");
if (count > 1) error->all(FLERR,"More than one fix shake");
// cannot use with minimization since SHAKE turns off bonds
// that should contribute to potential energy
if (update->whichflag == 2)
error->all("Fix shake cannot be used with minimization");
error->all(FLERR,"Fix shake cannot be used with minimization");
// error if npt,nph fix comes before shake fix
@ -297,7 +295,7 @@ void FixShake::init()
if (i < modify->nfix) {
for (int j = i; j < modify->nfix; j++)
if (strcmp(modify->fix[j]->style,"shake") == 0)
error->all("Shake fix must come before NPT/NPH fix");
error->all(FLERR,"Shake fix must come before NPT/NPH fix");
}
// if rRESPA, find associated fix that must exist
@ -315,7 +313,7 @@ void FixShake::init()
// set equilibrium bond distances
if (force->bond == NULL)
error->all("Bond potential must be defined for SHAKE");
error->all(FLERR,"Bond potential must be defined for SHAKE");
for (i = 1; i <= atom->nbondtypes; i++)
bond_distance[i] = force->bond->equilibrium_distance(i);
@ -326,7 +324,7 @@ void FixShake::init()
for (i = 1; i <= atom->nangletypes; i++) {
if (angle_flag[i] == 0) continue;
if (force->angle == NULL)
error->all("Angle potential must be defined for SHAKE");
error->all(FLERR,"Angle potential must be defined for SHAKE");
// scan all atoms for a SHAKE angle cluster
// extract bond types for the 2 bonds in the cluster
@ -353,7 +351,7 @@ void FixShake::init()
// error check for any bond types that are not the same
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_MAX,world);
if (flag_all) error->all("Shake angles have different bond types");
if (flag_all) error->all(FLERR,"Shake angles have different bond types");
// insure all procs have bond types
@ -458,7 +456,7 @@ void FixShake::pre_neighbor()
sprintf(str,
"Shake atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],me,update->ntimestep);
error->one(str);
error->one(FLERR,str);
}
if (i <= atom1 && i <= atom2) list[nlist++] = i;
} else if (shake_flag[i] % 2 == 1) {
@ -472,7 +470,7 @@ void FixShake::pre_neighbor()
BIGINT_FORMAT,
shake_atom[i][0],shake_atom[i][1],shake_atom[i][2],
me,update->ntimestep);
error->one(str);
error->one(FLERR,str);
}
if (i <= atom1 && i <= atom2 && i <= atom3) list[nlist++] = i;
} else {
@ -488,7 +486,7 @@ void FixShake::pre_neighbor()
shake_atom[i][0],shake_atom[i][1],
shake_atom[i][2],shake_atom[i][3],
me,update->ntimestep);
error->one(str);
error->one(FLERR,str);
}
if (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)
list[nlist++] = i;
@ -813,7 +811,7 @@ void FixShake::find_clusters()
}
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all) error->all("Did not find fix shake partner info");
if (flag_all) error->all(FLERR,"Did not find fix shake partner info");
// -----------------------------------------------------
// identify SHAKEable bonds
@ -947,7 +945,7 @@ void FixShake::find_clusters()
flag = 0;
for (i = 0; i < nlocal; i++) if (nshake[i] > 3) flag = 1;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all) error->all("Shake cluster of more than 4 atoms");
if (flag_all) error->all(FLERR,"Shake cluster of more than 4 atoms");
flag = 0;
for (i = 0; i < nlocal; i++) {
@ -956,7 +954,7 @@ void FixShake::find_clusters()
if (partner_shake[i][j] && partner_nshake[i][j] > 1) flag = 1;
}
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all) error->all("Shake clusters are connected");
if (flag_all) error->all(FLERR,"Shake clusters are connected");
// -----------------------------------------------------
// set SHAKE arrays that are stored with atoms & add angle constraints
@ -1349,7 +1347,7 @@ void FixShake::shake2(int m)
double determ = b*b - 4.0*a*c;
if (determ < 0.0) {
error->warning("Shake determinant < 0.0",0);
error->warning(FLERR,"Shake determinant < 0.0",0);
determ = 0.0;
}
@ -1469,7 +1467,7 @@ void FixShake::shake3(int m)
// inverse of matrix
double determ = a11*a22 - a12*a21;
if (determ == 0.0) error->one("Shake determinant = 0.0");
if (determ == 0.0) error->one(FLERR,"Shake determinant = 0.0");
double determinv = 1.0/determ;
double a11inv = a22*determinv;
@ -1663,7 +1661,7 @@ void FixShake::shake4(int m)
double determ = a11*a22*a33 + a12*a23*a31 + a13*a21*a32 -
a11*a23*a32 - a12*a21*a33 - a13*a22*a31;
if (determ == 0.0) error->one("Shake determinant = 0.0");
if (determ == 0.0) error->one(FLERR,"Shake determinant = 0.0");
double determinv = 1.0/determ;
double a11inv = determinv * (a22*a33 - a23*a32);
@ -1903,7 +1901,7 @@ void FixShake::shake3angle(int m)
double determ = a11*a22*a33 + a12*a23*a31 + a13*a21*a32 -
a11*a23*a32 - a12*a21*a33 - a13*a22*a31;
if (determ == 0.0) error->one("Shake determinant = 0.0");
if (determ == 0.0) error->one(FLERR,"Shake determinant = 0.0");
double determinv = 1.0/determ;
double a11inv = determinv * (a22*a33 - a23*a32);