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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4690 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2010-09-06 16:19:47 +00:00
parent de59192f5e
commit 8f02ff3b29
13 changed files with 71 additions and 60 deletions
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4
src/MANYBODY/pair_comb.cpp
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@ -691,7 +691,7 @@ void PairComb::read_file(char *file)
params[nparams].powermint = int(params[nparams].powerm);
// parameter set sanity checks
// parameter sanity checks
if (params[nparams].lam11 < 0.0 || params[nparams].lam12 < 0.0 ||
params[nparams].c < 0.0 || params[nparams].d < 0.0 ||
@ -723,7 +723,7 @@ void PairComb::read_file(char *file)
params[nparams].lam12 < params[nparams].lam22 ||
params[nparams].biga1< params[nparams].bigb1 ||
params[nparams].biga2< params[nparams].bigb2)
error->all("Improper COMB pair parameters");
error->all("Illegal COMB parameter");
nparams++;
}

2
src/PERI/fix_peri_neigh.cpp
View File

@ -281,8 +281,6 @@ void FixPeriNeigh::setup(int vflag)
else if (pairlps != NULL) // call the PairPeriLPS influence function
wvolume[i] += pairlps->influence_function(delx0,dely0,delz0) *
rsq0 * vfrac[j] * vfrac_scale;
else
error->all("Unknown peridynamic pair style in FixPeriNeigh.");
}
}

75
src/PERI/pair_peri_lps.cpp
View File

@ -59,7 +59,8 @@ PairPeriLPS::PairPeriLPS(LAMMPS *lmp) : Pair(lmp)
// set comm size needed by this Pair
// comm_reverse not needed
comm_forward = 1; // For passing dilatation (theta)
comm_forward = 1; // for passing dilatation (theta)
}
/* ---------------------------------------------------------------------- */
@ -287,10 +288,14 @@ void PairPeriLPS::compute(int eflag, int vflag)
(1.0 + ((delta - half_lc)/(2*half_lc) ) );
else vfrac_scale = 1.0;
omega_plus = influence_function(-1.0*delx0,-1.0*dely0,-1.0*delz0);
omega_minus = influence_function(delx0,dely0,delz0);
rk = ( (3.0 * bulkmodulus[itype][itype]) - (5.0 * shearmodulus[itype][itype]) ) * vfrac[j] * vfrac_scale * ( (omega_plus * theta[i] / wvolume[i]) + ( omega_minus * theta[j] / wvolume[j] ) ) * r0[i][jj] ;
rk += 15.0 * ( shearmodulus[itype][itype] * vfrac[j] * vfrac_scale ) * ( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) * dr;
omega_plus = influence_function(-1.0*delx0,-1.0*dely0,-1.0*delz0);
omega_minus = influence_function(delx0,dely0,delz0);
rk = ( (3.0 * bulkmodulus[itype][itype]) -
(5.0 * shearmodulus[itype][itype]) ) * vfrac[j] * vfrac_scale *
( (omega_plus * theta[i] / wvolume[i]) +
( omega_minus * theta[j] / wvolume[j] ) ) * r0[i][jj];
rk += 15.0 * ( shearmodulus[itype][itype] * vfrac[j] * vfrac_scale ) *
( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) * dr;
if (r > 0.0) fbond = -(rk/r);
else fbond = 0.0;
@ -302,7 +307,9 @@ void PairPeriLPS::compute(int eflag, int vflag)
// since I-J is double counted, set newton off & use 1/2 factor and I,I
double deviatoric_extension = dr - (theta[i]* r0[i][jj] / 3.0);
if (eflag) evdwl = 0.5 * 15 * (shearmodulus[itype][itype]/wvolume[i]) * omega_plus * ( deviatoric_extension * deviatoric_extension ) * vfrac[j] * vfrac_scale;
if (eflag) evdwl = 0.5 * 15 * (shearmodulus[itype][itype]/wvolume[i]) *
omega_plus*(deviatoric_extension * deviatoric_extension) *
vfrac[j] * vfrac_scale;
if (evflag) ev_tally(i,i,nlocal,0,
0.5*evdwl,0.0,0.5*fbond,delx,dely,delz);
@ -346,8 +353,8 @@ void PairPeriLPS::allocate()
setflag[i][j] = 0;
cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq");
bulkmodulus = memory->create_2d_double_array(n+1,n+1,"pair:bulkmodulus");
shearmodulus = memory->create_2d_double_array(n+1,n+1,"pair:shearmodulus");
bulkmodulus = memory->create_2d_double_array(n+1,n+1,"pair:bulkmodulus");
shearmodulus = memory->create_2d_double_array(n+1,n+1,"pair:shearmodulus");
s00 = memory->create_2d_double_array(n+1,n+1,"pair:s00");
alpha = memory->create_2d_double_array(n+1,n+1,"pair:alpha");
cut = memory->create_2d_double_array(n+1,n+1,"pair:cut");
@ -514,8 +521,8 @@ void PairPeriLPS::read_restart(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairPeriLPS::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj,
double PairPeriLPS::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
double &fforce)
{
double delx0,dely0,delz0,rsq0;
@ -547,10 +554,10 @@ double PairPeriLPS::single(int i, int j, int itype, int jtype, double rsq,
if (r < d_ij) {
dr = r - d_ij;
// kshort resembles the short-range force constant of the bond-based theory in 3-D !
kshort = (15.0 * 18.0 * bulkmodulus[itype][itype]) /
( 3.141592653589793 * cutsq[itype][jtype] * cutsq[itype][jtype] );
rk = ( kshort * vfrac[j]) * (dr / sqrt(cutsq[itype][jtype]));
// kshort resembles short-range force constant of bond-based theory in 3d
kshort = (15.0 * 18.0 * bulkmodulus[itype][itype]) /
( 3.141592653589793 * cutsq[itype][jtype] * cutsq[itype][jtype]);
rk = ( kshort * vfrac[j]) * (dr / sqrt(cutsq[itype][jtype]));
if (r > 0.0) fforce += -(rk/r);
energy += 0.5*rk*dr;
}
@ -587,13 +594,19 @@ double PairPeriLPS::single(int i, int j, int itype, int jtype, double rsq,
(1.0 + ((sqrt(cutsq[itype][jtype]) - half_lc)/(2*half_lc)));
else vfrac_scale = 1.0;
omega_plus = influence_function(-1.0*delx0,-1.0*dely0,-1.0*delz0);
omega_plus = influence_function(-1.0*delx0,-1.0*dely0,-1.0*delz0);
omega_minus = influence_function(delx0,dely0,delz0);
rk = (3.0* bulkmodulus[itype][itype] -5.0 * shearmodulus[itype][itype] )* vfrac[j] * vfrac_scale * ( (omega_plus * theta[i] / wvolume[i]) + ( omega_minus * theta[j] / wvolume[j] ) ) * r0[i][jj] ;
rk += 15.0 * ( shearmodulus[itype][itype] * vfrac[j] * vfrac_scale ) * ( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) * dr;
rk = (3.0* bulkmodulus[itype][itype] -5.0 * shearmodulus[itype][itype]) *
vfrac[j] * vfrac_scale * ( (omega_plus * theta[i] / wvolume[i]) +
(omega_minus * theta[j] / wvolume[j])) *
r0[i][jj];
rk += 15.0 * ( shearmodulus[itype][itype] * vfrac[j] * vfrac_scale ) *
( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) * dr;
if (r > 0.0) fforce += -(rk/r);
energy += 0.5 * 15 * (shearmodulus[itype][itype]/wvolume[i]) * omega_plus * ( dr - theta[i]* r0[i][jj] / 3.0 ) * ( dr - theta[i]* r0[i][jj] / 3.0 ) * vfrac[j] * vfrac_scale;
energy += 0.5 * 15 * (shearmodulus[itype][itype]/wvolume[i]) *
omega_plus * ( dr - theta[i]* r0[i][jj] / 3.0 ) *
( dr - theta[i]* r0[i][jj] / 3.0 ) * vfrac[j] * vfrac_scale;
}
}
@ -612,7 +625,7 @@ double PairPeriLPS::memory_usage()
}
/* ----------------------------------------------------------------------
Influence function definition
influence function definition
------------------------------------------------------------------------- */
double PairPeriLPS::influence_function(double xi_x, double xi_y, double xi_z)
@ -620,10 +633,9 @@ double PairPeriLPS::influence_function(double xi_x, double xi_y, double xi_z)
double r = sqrt(xi_x*xi_x + xi_y*xi_y + xi_z*xi_z);
double omega;
if (fabs(r) < 2.2204e-016) error->one("pair_peri_lps - influence_function: Divide by 0");
if (fabs(r) < 2.2204e-016)
error->one("Divide by 0 in influence function of pair peri/lps");
omega = 1.0/r;
return omega;
}
@ -655,7 +667,7 @@ void PairPeriLPS::compute_dilatation()
int nonperiodic = domain->nonperiodic;
// compute the dilatation theta
// loop over my particles
for (i = 0; i < nlocal; i++) {
xtmp = x[i][0];
ytmp = x[i][1];
@ -667,7 +679,6 @@ void PairPeriLPS::compute_dilatation()
theta[i] = 0.0;
itype = type[i];
// loop over partners of particle i
for (jj = 0; jj < jnum; jj++) {
// if bond already broken, skip this partner
@ -704,23 +715,25 @@ void PairPeriLPS::compute_dilatation()
(1.0 + ((delta - half_lc)/(2*half_lc) ) );
else vfrac_scale = 1.0;
theta[i] += influence_function(delx0, dely0, delz0) * r0[i][jj] * dr * vfrac[j] * vfrac_scale;
theta[i] += influence_function(delx0, dely0, delz0) * r0[i][jj] * dr *
vfrac[j] * vfrac_scale;
} // end loop over all neighbors jj
}
// if wvolume[i] is zero, then particle i has no bonds
// therefore, the dilatation is set to
// If wvolume[i] is zero, then particle i has no bonds. Therefore, the dilatation is set to 0.
if (wvolume[i] != 0.0) theta[i] = (3.0/wvolume[i]) * theta[i];
else theta[i] = 0;
} // end loop over all particles i
}
}
/* ----------------------------------------------------------------------
communication routines
---------------------------------------------------------------------- */
int PairPeriLPS::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
int PairPeriLPS::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;

2
src/compute_temp_region.cpp
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@ -68,7 +68,7 @@ void ComputeTempRegion::init()
iregion = domain->find_region(idregion);
if (iregion == -1)
error->all("Region ID for temp reduce/region does not exist");
error->all("Region ID for compute temp reduce/region does not exist");
dof = 0.0;
}

4
src/fix_adapt.cpp
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@ -164,14 +164,14 @@ void FixAdapt::init()
if (strcmp(param[m],"diameter") == 0) {
awhich[m] = DIAMETER;
if (!atom->radius_flag)
error->all("Fix adapt requires atom attribute radius");
error->all("Fix adapt requires atom attribute diameter");
} else error->all("Fix adapt atom attribute is not recognized");
}
ivar[m] = input->variable->find(var[m]);
if (ivar[m] < 0) error->all("Variable name for fix adapt does not exist");
if (!input->variable->equalstyle(ivar[m]))
error->all("Variable for fix adapt is not equal style");
error->all("Variable for fix adapt is invalid style");
}
}

4
src/fix_box_relax.cpp
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@ -219,7 +219,7 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
if (pcouple == XYZ && dimension == 3 &&
(p_target[0] != p_target[1] || p_target[0] != p_target[2]))
error->all("Invalid fix nvt/npt/nph pressure settings");
error->all("Invalid fix box/relax pressure settings");
if (pcouple == XYZ && dimension == 2 && p_target[0] != p_target[1])
error->all("Invalid fix box/relax pressure settings");
if (pcouple == XY && p_target[0] != p_target[1])
@ -611,7 +611,7 @@ void FixBoxRelax::remap()
domain->boxlo[i] = currentBoxLo0 + (currentBoxLo0-ctr)*ds[i]/s0[i];
domain->boxhi[i] = currentBoxHi0 + (currentBoxHi0-ctr)*ds[i]/s0[i];
if (domain->boxlo[i] >= domain->boxhi[i])
error->all("fix box/relax generated negative dimension");
error->all("Fix box/relax generated negative box length");
}
if (pstyle == TRICLINIC) {

2
src/fix_indent.cpp
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@ -116,7 +116,7 @@ void FixIndent::init()
xvar = input->variable->find(xstr);
if (xvar < 0) error->all("Variable name for fix indent does not exist");
if (!input->variable->equalstyle(xvar))
error->all("Variable for fix indent is not equal style");
error->all("Variable for fix indent is invalid style");
}
if (ystr) {
yvar = input->variable->find(ystr);

2
src/fix_nh.cpp
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@ -96,7 +96,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
t_stop = atof(arg[iarg+2]);
t_period = atof(arg[iarg+3]);
if (t_start < 0.0 || t_stop <= 0.0)
error->all("Target T for fix nvt/npt/nph cannot be 0.0");
error->all("Target temperature for fix nvt/npt/nph cannot be 0.0");
iarg += 4;
} else if (strcmp(arg[iarg],"iso") == 0) {

2
src/fix_nh_sphere.cpp
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@ -36,7 +36,7 @@ FixNHSphere::FixNHSphere(LAMMPS *lmp, int narg, char **arg) :
"atom attributes omega, torque");
if (!atom->radius_flag && !atom->avec->shape_type)
error->all("Fix nvt/nph/npt sphere requires "
"atom attribute radius or shape");
"atom attribute diameter or shape");
}
/* ---------------------------------------------------------------------- */

2
src/fix_nve_sphere.cpp
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@ -56,7 +56,7 @@ FixNVESphere::FixNVESphere(LAMMPS *lmp, int narg, char **arg) :
if (!atom->omega_flag || !atom->torque_flag)
error->all("Fix nve/sphere requires atom attributes omega, torque");
if (!atom->radius_flag && !atom->avec->shape_type)
error->all("Fix nve/sphere requires atom attribute radius or shape");
error->all("Fix nve/sphere requires atom attribute diameter or shape");
if (extra == DIPOLE && !atom->mu_flag)
error->all("Fix nve/sphere requires atom attribute mu");
}

18
src/fix_press_berendsen.cpp
View File

@ -116,7 +116,7 @@ FixPressBerendsen::FixPressBerendsen(LAMMPS *lmp, int narg, char **arg) :
p_flag[2] = 1;
iarg += 4;
if (dimension == 2)
error->all("Invalid fix press/berendsen command for a 2d simulation");
error->all("Invalid fix press/berendsen for a 2d simulation");
} else if (strcmp(arg[iarg],"couple") == 0) {
if (iarg+2 > narg) error->all("Illegal fix press/berendsen command");
@ -148,20 +148,20 @@ FixPressBerendsen::FixPressBerendsen(LAMMPS *lmp, int narg, char **arg) :
// error checks
if (dimension == 2 && p_flag[2])
error->all("Invalid fix press/berendsen command for a 2d simulation");
error->all("Invalid fix press/berendsen for a 2d simulation");
if (dimension == 2 && (pcouple == YZ || pcouple == XZ))
error->all("Invalid fix press/berendsen command for a 2d simulation");
error->all("Invalid fix press/berendsen for a 2d simulation");
if (pcouple == XYZ && (p_flag[0] == 0 || p_flag[1] == 0))
error->all("Invalid fix press/berendsen command pressure settings");
error->all("Invalid fix press/berendsen pressure settings");
if (pcouple == XYZ && dimension == 3 && p_flag[2] == 0)
error->all("Invalid fix press/berendsen command pressure settings");
error->all("Invalid fix press/berendsen pressure settings");
if (pcouple == XY && (p_flag[0] == 0 || p_flag[1] == 0))
error->all("Invalid fix press/berendsen command pressure settings");
error->all("Invalid fix press/berendsen pressure settings");
if (pcouple == YZ && (p_flag[1] == 0 || p_flag[2] == 0))
error->all("Invalid fix press/berendsen command pressure settings");
error->all("Invalid fix press/berendsen pressure settings");
if (pcouple == XZ && (p_flag[0] == 0 || p_flag[2] == 0))
error->all("Invalid fix press/berendsen command pressure settings");
error->all("Invalid fix press/berendsen pressure settings");
if (p_flag[0] && domain->xperiodic == 0)
error->all("Cannot use fix press/berendsen on a non-periodic dimension");
@ -178,7 +178,7 @@ FixPressBerendsen::FixPressBerendsen(LAMMPS *lmp, int narg, char **arg) :
if (pcouple == XYZ && dimension == 2 &&
(p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
p_period[0] != p_period[1]))
error->all("Invalid fix press_berendsen pressure settings");
error->all("Invalid fix press/berendsen pressure settings");
if (pcouple == XY &&
(p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
p_period[0] != p_period[1]))

2
src/fix_rigid.cpp
View File

@ -1332,7 +1332,7 @@ void FixRigid::no_squish_rotate(int k, double *p, double *q,
kq[1] = q[2]; kp[1] = p[2];
kq[2] = -q[1]; kp[2] = -p[1];
kq[3] = q[0]; kp[3] = p[0];
} else error->all("Invalid no-squish rotate pivot value");
}
// obtain phi, cosines and sines

12
src/fix_wall_reflect.cpp
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@ -210,42 +210,42 @@ void FixWallReflect::init()
if (xlovar < 0)
error->all("Variable name for fix wall/relect does not exist");
if (!input->variable->equalstyle(xlovar))
error->all("Variable for fix wall/reflect is not equal style");
error->all("Variable for fix wall/reflect is invalid style");
}
if (xhistr) {
xhivar = input->variable->find(xhistr);
if (xhivar < 0)
error->all("Variable name for fix wall/relect does not exist");
if (!input->variable->equalstyle(xhivar))
error->all("Variable for fix wall/reflect is not equal style");
error->all("Variable for fix wall/reflect is invalid style");
}
if (ylostr) {
ylovar = input->variable->find(ylostr);
if (ylovar < 0)
error->all("Variable name for fix wall/relect does not exist");
if (!input->variable->equalstyle(ylovar))
error->all("Variable for fix wall/reflect is not equal style");
error->all("Variable for fix wall/reflect is invalid style");
}
if (yhistr) {
yhivar = input->variable->find(yhistr);
if (yhivar < 0)
error->all("Variable name for fix wall/relect does not exist");
if (!input->variable->equalstyle(yhivar))
error->all("Variable for fix wall/reflect is not equal style");
error->all("Variable for fix wall/reflect is invalid style");
}
if (zlostr) {
zlovar = input->variable->find(zlostr);
if (zlovar < 0)
error->all("Variable name for fix wall/relect does not exist");
if (!input->variable->equalstyle(zlovar))
error->all("Variable for fix wall/reflect is not equal style");
error->all("Variable for fix wall/reflect is invalid style");
}
if (zhistr) {
zhivar = input->variable->find(zhistr);
if (zhivar < 0)
error->all("Variable name for fix wall/relect does not exist");
if (!input->variable->equalstyle(zhivar))
error->all("Variable for fix wall/reflect is not equal style");
error->all("Variable for fix wall/reflect is invalid style");
}
int nrigid = 0;