From 17f9667059fe2ac0fe097401c1bc38dc1b4b2f4d Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Wed, 13 Apr 2011 21:40:28 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5933
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
bench/in.chute | 2 +-
bench/in.chute.scaled | 2 +-
examples/colloid/in.colloid | 6 +-
examples/dipole/in.dipole | 8 +-
examples/ellipse/in.ellipse.gayberne | 8 +-
examples/ellipse/in.ellipse.resquared | 8 +-
examples/pour/in.pour | 2 +-
examples/pour/in.pour.2d | 2 +-
examples/srd/in.srd.mixture | 11 +-
tools/restart2data.cpp | 148 ++++++++++++--------------
10 files changed, 93 insertions(+), 104 deletions(-)
diff --git a/bench/in.chute b/bench/in.chute
index 985f4140e2..cf43fd7ff8 100644
--- a/bench/in.chute
+++ b/bench/in.chute
@@ -2,7 +2,7 @@
# chute flow of 32000 atoms with frozen base at 26 degrees
units lj
-atom_style granular
+atom_style sphere
boundary p p fs
newton off
communicate single vel yes
diff --git a/bench/in.chute.scaled b/bench/in.chute.scaled
index 583fd70d67..cda2445620 100644
--- a/bench/in.chute.scaled
+++ b/bench/in.chute.scaled
@@ -5,7 +5,7 @@ variable x index 1
variable y index 1
units lj
-atom_style granular
+atom_style sphere
boundary p p fs
newton off
communicate single vel yes
diff --git a/examples/colloid/in.colloid b/examples/colloid/in.colloid
index 6d3229de3e..5265cf1007 100644
--- a/examples/colloid/in.colloid
+++ b/examples/colloid/in.colloid
@@ -1,7 +1,7 @@
# Big colloid particles and small LJ particles
units lj
-atom_style atomic
+atom_style sphere
dimension 2
lattice sq 0.01
@@ -11,8 +11,8 @@ create_atoms 1 box
set group all type/fraction 2 0.96 23984
-mass 1 9
-mass 2 1
+set type 1 mass 9
+set type 2 mass 1
velocity all create 1.44 87287 loop geom
diff --git a/examples/dipole/in.dipole b/examples/dipole/in.dipole
index b98a9f521b..c8f6e887e8 100644
--- a/examples/dipole/in.dipole
+++ b/examples/dipole/in.dipole
@@ -1,7 +1,7 @@
# Point dipoles in a 2d box
units lj
-atom_style dipole
+atom_style hybrid sphere dipole
dimension 2
lattice sq2 0.7
@@ -9,10 +9,8 @@ region box block 0 10 0 10 -0.5 0.5
create_box 1 box
create_atoms 1 box
-mass 1 1.0
-shape 1 1 1 1
-dipole 1 0.75
-set group all dipole/random 98934
+set group all mass 1.0
+set group all dipole/random 98934 0.75
velocity all create 0.0 87287 mom no
diff --git a/examples/ellipse/in.ellipse.gayberne b/examples/ellipse/in.ellipse.gayberne
index b739082994..a78c9c55b1 100644
--- a/examples/ellipse/in.ellipse.gayberne
+++ b/examples/ellipse/in.ellipse.gayberne
@@ -12,10 +12,10 @@ create_atoms 1 box
set group all type/fraction 2 0.1 95392
set group all quat/random 18238
-mass 1 1.0
-mass 2 1.5
-shape 1 1 1 1
-shape 2 3 1 1
+set type 1 mass 1.0
+set type 2 mass 1.5
+set type 1 shape 1 1 1
+set type 2 shape 3 1 1
compute rot all temp/asphere
group spheroid type 1
diff --git a/examples/ellipse/in.ellipse.resquared b/examples/ellipse/in.ellipse.resquared
index c7a2030f9e..2bbe76c2a0 100644
--- a/examples/ellipse/in.ellipse.resquared
+++ b/examples/ellipse/in.ellipse.resquared
@@ -12,10 +12,10 @@ create_atoms 1 box
set group all type/fraction 2 0.1 95392
set group all quat/random 18238
-mass 1 1.0
-mass 2 1.5
-shape 1 1 1 1
-shape 2 3 1 1
+set type 1 mass 1.0
+set type 2 mass 1.5
+set type 1 shape 1 1 1
+set type 2 shape 3 1 1
compute rot all temp/asphere
group spheroid type 1
diff --git a/examples/pour/in.pour b/examples/pour/in.pour
index 3d29938cf1..a0e58db342 100644
--- a/examples/pour/in.pour
+++ b/examples/pour/in.pour
@@ -1,6 +1,6 @@
# Pour granular particles into chute container, then induce flow
-atom_style granular
+atom_style sphere
boundary p p fm
newton off
communicate single vel yes
diff --git a/examples/pour/in.pour.2d b/examples/pour/in.pour.2d
index 3be3af2fe4..ae38792939 100644
--- a/examples/pour/in.pour.2d
+++ b/examples/pour/in.pour.2d
@@ -1,7 +1,7 @@
# Pour 2d granular particles into container
dimension 2
-atom_style granular
+atom_style sphere
boundary f fm p
newton off
communicate single vel yes
diff --git a/examples/srd/in.srd.mixture b/examples/srd/in.srd.mixture
index 77d95eac0b..8bcc48d311 100644
--- a/examples/srd/in.srd.mixture
+++ b/examples/srd/in.srd.mixture
@@ -1,7 +1,7 @@
# 2d SRD test: big + small particles
units lj
-atom_style colloid
+atom_style sphere
atom_modify first big
dimension 2
@@ -11,11 +11,8 @@ lattice sq 0.4
region box block 0 10 0 10 -0.5 0.5
create_box 2 box
create_atoms 1 region box
-mass 1 1.0
-mass 2 0.01
-
-shape 1 1.0 1.0 1.0
-shape 2 0.0 0.0 0.0
+set type 1 mass 1.0
+set type 1 diameter 1.0
group big type 1
velocity big create 1.44 87287 loop geom
@@ -44,6 +41,8 @@ lattice sq 0.4
region plane block 0 10 0 10 -0.001 0.001
lattice sq 85.0
create_atoms 2 region plane
+set type 2 mass 0.01
+set type 2 diameter 0.0
group small type 2
diff --git a/tools/restart2data.cpp b/tools/restart2data.cpp
index 79c9a16453..28602809ee 100644
--- a/tools/restart2data.cpp
+++ b/tools/restart2data.cpp
@@ -33,6 +33,7 @@
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#define MAX_GROUP 32
+#define PI 4.0*atan(1.0)
// these should match settings in src/lmptype.h
@@ -47,19 +48,19 @@ typedef int64_t bigint;
// same as write_restart.cpp
enum{VERSION,SMALLINT,TAGINT,BIGINT,
- UNITS,NTIMESTEP,DIMENSION,NPROCS,PROCGRID_0,PROCGRID_1,PROCGRID_2,
- NEWTON_PAIR,NEWTON_BOND,XPERIODIC,YPERIODIC,ZPERIODIC,
- BOUNDARY_00,BOUNDARY_01,BOUNDARY_10,BOUNDARY_11,BOUNDARY_20,BOUNDARY_21,
- ATOM_STYLE,NATOMS,NTYPES,
- NBONDS,NBONDTYPES,BOND_PER_ATOM,
- NANGLES,NANGLETYPES,ANGLE_PER_ATOM,
- NDIHEDRALS,NDIHEDRALTYPES,DIHEDRAL_PER_ATOM,
- NIMPROPERS,NIMPROPERTYPES,IMPROPER_PER_ATOM,
- BOXLO_0,BOXHI_0,BOXLO_1,BOXHI_1,BOXLO_2,BOXHI_2,
- SPECIAL_LJ_1,SPECIAL_LJ_2,SPECIAL_LJ_3,
- SPECIAL_COUL_1,SPECIAL_COUL_2,SPECIAL_COUL_3,
- XY,XZ,YZ};
-enum{MASS,SHAPE,DIPOLE};
+ UNITS,NTIMESTEP,DIMENSION,NPROCS,PROCGRID_0,PROCGRID_1,PROCGRID_2,
+ NEWTON_PAIR,NEWTON_BOND,XPERIODIC,YPERIODIC,ZPERIODIC,
+ BOUNDARY_00,BOUNDARY_01,BOUNDARY_10,BOUNDARY_11,BOUNDARY_20,BOUNDARY_21,
+ ATOM_STYLE,NATOMS,NTYPES,
+ NBONDS,NBONDTYPES,BOND_PER_ATOM,
+ NANGLES,NANGLETYPES,ANGLE_PER_ATOM,
+ NDIHEDRALS,NDIHEDRALTYPES,DIHEDRAL_PER_ATOM,
+ NIMPROPERS,NIMPROPERTYPES,IMPROPER_PER_ATOM,
+ BOXLO_0,BOXHI_0,BOXLO_1,BOXHI_1,BOXLO_2,BOXHI_2,
+ SPECIAL_LJ_1,SPECIAL_LJ_2,SPECIAL_LJ_3,
+ SPECIAL_COUL_1,SPECIAL_COUL_2,SPECIAL_COUL_3,
+ XY,XZ,YZ};
+enum{MASS};
enum{PAIR,BOND,ANGLE,DIHEDRAL,IMPROPER};
static const char * const cg_type_list[] =
@@ -87,8 +88,8 @@ class Data {
char *atom_style;
int style_angle,style_atomic,style_bond,style_charge,style_dipole;
- int style_ellipsoid,style_full,style_granular;
- int style_hybrid,style_molecular,style_peri;
+ int style_ellipsoid,style_full;
+ int style_hybrid,style_molecular,style_peri,style_sphere;
bigint natoms;
bigint nbonds,nangles,ndihedrals,nimpropers;
@@ -191,7 +192,7 @@ class Data {
int iatoms,ibonds,iangles,idihedrals,iimpropers;
- double *mass,*shape,*dipole;
+ double *mass;
double *x,*y,*z,*vx,*vy,*vz;
double *omegax,*omegay,*omegaz;
tagint *tag;
@@ -199,6 +200,7 @@ class Data {
int *molecule;
double *q,*mux,*muy,*muz,*radius,*density,*vfrac,*rmass;
double *s0,*x0x,*x0y,*x0z;
+ double *shapex,*shapey,*shapez;
double *quatw,*quati,*quatj,*quatk,*angmomx,*angmomy,*angmomz;
int *bond_type,*angle_type,*dihedral_type,*improper_type;
int *bond_atom1,*bond_atom2;
@@ -219,9 +221,9 @@ class Data {
void write_atom_dipole(FILE *, int, int, int, int);
void write_atom_ellipsoid(FILE *, int, int, int, int);
void write_atom_full(FILE *, int, int, int, int);
- void write_atom_granular(FILE *, int, int, int, int);
void write_atom_molecular(FILE *, int, int, int, int);
void write_atom_peri(FILE *, int, int, int, int);
+ void write_atom_sphere(FILE *, int, int, int, int);
void write_atom_angle_extra(FILE *, int);
void write_atom_atomic_extra(FILE *, int);
@@ -230,9 +232,9 @@ class Data {
void write_atom_dipole_extra(FILE *, int);
void write_atom_ellipsoid_extra(FILE *, int);
void write_atom_full_extra(FILE *, int);
- void write_atom_granular_extra(FILE *, int);
void write_atom_molecular_extra(FILE *, int);
void write_atom_peri_extra(FILE *, int);
+ void write_atom_sphere_extra(FILE *, int);
void write_vel_angle(FILE *, int);
void write_vel_atomic(FILE *, int);
@@ -241,9 +243,9 @@ class Data {
void write_vel_dipole(FILE *, int);
void write_vel_ellipsoid(FILE *, int);
void write_vel_full(FILE *, int);
- void write_vel_granular(FILE *, int);
void write_vel_molecular(FILE *, int);
void write_vel_peri(FILE *, int);
+ void write_vel_sphere(FILE *, int);
void write_vel_angle_extra(FILE *, int);
void write_vel_atomic_extra(FILE *, int);
@@ -252,9 +254,9 @@ class Data {
void write_vel_dipole_extra(FILE *, int);
void write_vel_ellipsoid_extra(FILE *, int);
void write_vel_full_extra(FILE *, int);
- void write_vel_granular_extra(FILE *, int);
void write_vel_molecular_extra(FILE *, int);
void write_vel_peri_extra(FILE *, int);
+ void write_vel_sphere_extra(FILE *, int);
};
// ---------------------------------------------------------------------
@@ -281,9 +283,9 @@ void allocate_charge(Data &data);
void allocate_dipole(Data &data);
void allocate_ellipsoid(Data &data);
void allocate_full(Data &data);
-void allocate_granular(Data &data);
void allocate_molecular(Data &data);
void allocate_peri(Data &data);
+void allocate_sphere(Data &data);
int atom_angle(double *, Data &, int);
int atom_atomic(double *, Data &, int);
@@ -292,9 +294,9 @@ int atom_charge(double *, Data &, int);
int atom_dipole(double *, Data &, int);
int atom_ellipsoid(double *, Data &, int);
int atom_full(double *, Data &, int);
-int atom_granular(double *, Data &, int);
int atom_molecular(double *, Data &, int);
int atom_peri(double *, Data &, int);
+int atom_sphere(double *, Data &, int);
int read_int(FILE *fp);
double read_double(FILE *fp);
@@ -484,8 +486,8 @@ void header(FILE *fp, Data &data)
else if (flag == ATOM_STYLE) {
data.style_angle = data.style_atomic = data.style_bond =
data.style_charge = data.style_dipole =
- data.style_ellipsoid = data.style_full = data.style_granular =
- data.style_hybrid = data.style_molecular = data.style_peri = 0;
+ data.style_ellipsoid = data.style_full = data.style_hybrid =
+ data.style_molecular = data.style_peri = data.style_sphere = 0;
data.atom_style = read_char(fp);
set_style(data.atom_style,data,1);
@@ -559,10 +561,10 @@ void set_style(char *name, Data &data, int flag)
else if (strcmp(name,"dipole") == 0) data.style_dipole = flag;
else if (strcmp(name,"ellipsoid") == 0) data.style_ellipsoid = flag;
else if (strcmp(name,"full") == 0) data.style_full = flag;
- else if (strcmp(name,"granular") == 0) data.style_granular = flag;
else if (strcmp(name,"hybrid") == 0) data.style_hybrid = flag;
else if (strcmp(name,"molecular") == 0) data.style_molecular = flag;
else if (strcmp(name,"peri") == 0) data.style_peri = flag;
+ else if (strcmp(name,"sphere") == 0) data.style_sphere = flag;
else {
printf("ERROR: Unknown atom style %s\n",name);
exit(1);
@@ -599,8 +601,6 @@ void groups(FILE *fp)
void type_arrays(FILE *fp, Data &data)
{
data.mass = NULL;
- data.shape = NULL;
- data.dipole = NULL;
int flag;
flag = read_int(fp);
@@ -610,12 +610,6 @@ void type_arrays(FILE *fp, Data &data)
if (flag == MASS) {
data.mass = new double[data.ntypes+1];
fread(&data.mass[1],sizeof(double),data.ntypes,fp);
- } else if (flag == SHAPE) {
- data.shape = new double[3*(data.ntypes+1)];
- fread(&data.shape[3],sizeof(double),3*data.ntypes,fp);
- } else if (flag == DIPOLE) {
- data.dipole = new double[data.ntypes+1];
- fread(&data.dipole[1],sizeof(double),data.ntypes,fp);
} else {
printf("ERROR: Invalid flag in type arrays section of restart file %d\n",
flag);
@@ -732,9 +726,9 @@ int atom(double *buf, Data &data)
if (data.style_dipole) allocate_dipole(data);
if (data.style_ellipsoid) allocate_ellipsoid(data);
if (data.style_full) allocate_full(data);
- if (data.style_granular) allocate_granular(data);
if (data.style_molecular) allocate_molecular(data);
if (data.style_peri) allocate_peri(data);
+ if (data.style_sphere) allocate_sphere(data);
}
// read atom quantities from buf
@@ -754,9 +748,9 @@ int atom(double *buf, Data &data)
if (k == data.style_dipole) m += atom_dipole(&buf[m],data,iatoms);
if (k == data.style_ellipsoid) m += atom_ellipsoid(&buf[m],data,iatoms);
if (k == data.style_full) m += atom_full(&buf[m],data,iatoms);
- if (k == data.style_granular) m += atom_granular(&buf[m],data,iatoms);
if (k == data.style_molecular) m += atom_molecular(&buf[m],data,iatoms);
if (k == data.style_peri) m += atom_peri(&buf[m],data,iatoms);
+ if (k == data.style_sphere) m += atom_sphere(&buf[m],data,iatoms);
}
data.iatoms++;
@@ -922,6 +916,15 @@ int atom_ellipsoid(double *buf, Data &data, int iatoms)
data.vy[iatoms] = buf[m++];
data.vz[iatoms] = buf[m++];
+ data.shapex[iatoms] = buf[m++];
+ data.shapey[iatoms] = buf[m++];
+ data.shapez[iatoms] = buf[m++];
+ data.rmass[iatoms] = buf[m++];
+ if (data.shapex[iatoms] == 0.0) data.density[iatoms] = data.rmass[iatoms];
+ else
+ data.density[iatoms] = data.rmass[iatoms] /
+ (4.0*PI/3.0 *
+ data.shapex[iatoms]*data.shapey[iatoms]*data.shapez[iatoms]);
data.quatw[iatoms] = buf[m++];
data.quati[iatoms] = buf[m++];
data.quatj[iatoms] = buf[m++];
@@ -933,7 +936,7 @@ int atom_ellipsoid(double *buf, Data &data, int iatoms)
return m;
}
-int atom_granular(double *buf, Data &data, int iatoms)
+int atom_sphere(double *buf, Data &data, int iatoms)
{
int m = 1;
data.x[iatoms] = buf[m++];
@@ -948,7 +951,12 @@ int atom_granular(double *buf, Data &data, int iatoms)
data.vz[iatoms] = buf[m++];
data.radius[iatoms] = buf[m++];
- data.density[iatoms] = buf[m++];
+ data.rmass[iatoms] = buf[m++];
+ if (data.radius[iatoms] == 0.0) data.density[iatoms] = data.rmass[iatoms];
+ else
+ data.density[iatoms] = data.rmass[iatoms] /
+ (4.0*PI/3.0 *
+ data.radius[iatoms]*data.radius[iatoms]*data.radius[iatoms]);
data.omegax[iatoms] = buf[m++];
data.omegay[iatoms] = buf[m++];
data.omegaz[iatoms] = buf[m++];
@@ -1136,7 +1144,6 @@ int atom_peri(double *buf, Data &data, int iatoms)
data.vz[iatoms] = buf[m++];
data.vfrac[iatoms] = buf[m++];
- data.density[iatoms] = buf[m++];
data.rmass[iatoms] = buf[m++];
data.s0[iatoms] = buf[m++];
data.x0x[iatoms] = buf[m++];
@@ -1211,6 +1218,11 @@ void allocate_full(Data &data)
void allocate_ellipsoid(Data &data)
{
+ data.shapex = new double[data.natoms];
+ data.shapey = new double[data.natoms];
+ data.shapez = new double[data.natoms];
+ data.rmass = new double[data.natoms];
+ data.density = new double[data.natoms];
data.quatw = new double[data.natoms];
data.quati = new double[data.natoms];
data.quatj = new double[data.natoms];
@@ -1220,9 +1232,10 @@ void allocate_ellipsoid(Data &data)
data.angmomz = new double[data.natoms];
}
-void allocate_granular(Data &data)
+void allocate_sphere(Data &data)
{
data.radius = new double[data.natoms];
+ data.rmass = new double[data.natoms];
data.density = new double[data.natoms];
data.omegax = new double[data.natoms];
data.omegay = new double[data.natoms];
@@ -1254,7 +1267,6 @@ void allocate_molecular(Data &data)
void allocate_peri(Data &data)
{
data.vfrac = new double[data.natoms];
- data.density = new double[data.natoms];
data.rmass = new double[data.natoms];
data.s0 = new double[data.natoms];
data.x0x = new double[data.natoms];
@@ -2708,21 +2720,6 @@ void Data::write(FILE *fp, FILE *fp2)
}
}
- // shape and dipole to data file
- // convert shape from radius to diameter
-
- if (shape) {
- fprintf(fp,"\nShapes\n\n");
- for (int i = 1; i <= ntypes; i++)
- fprintf(fp,"%d %g %g %g\n",i,
- 2.0*shape[3*i+0],2.0*shape[3*i+1],2.0*shape[3*i+2]);
- }
-
- if (dipole) {
- fprintf(fp,"\nDipoles\n\n");
- for (int i = 1; i <= ntypes; i++) fprintf(fp,"%d %g\n",i,dipole[i]);
- }
-
// pair coeffs to data file
if (pair_style && fp2 == NULL) {
@@ -2962,8 +2959,6 @@ void Data::write(FILE *fp, FILE *fp2)
// angle coeffs to data file
if (angle_style && fp2 == NULL) {
- double PI = 3.1415926; // convert back to degrees
-
if ((strcmp(angle_style,"none") != 0) &&
(strcmp(angle_style,"table") != 0) &&
(strcmp(angle_style,"hybrid") != 0))
@@ -3022,8 +3017,6 @@ void Data::write(FILE *fp, FILE *fp2)
// only supported styles = cosine/squared, harmonic, cg/cmm
if (angle_style && fp2) {
- double PI = 3.1415926; // convert back to degrees
-
if ((strcmp(angle_style,"cosine/squared") == 0) ||
(strcmp(angle_style,"cosine/delta") == 0)) {
for (int i = 1; i <= nangletypes; i++)
@@ -3051,8 +3044,6 @@ void Data::write(FILE *fp, FILE *fp2)
}
if (dihedral_style) {
- double PI = 3.1415926; // convert back to degrees
-
if ((strcmp(dihedral_style,"none") != 0) &&
(strcmp(dihedral_style,"table") != 0) &&
(strcmp(dihedral_style,"hybrid") != 0))
@@ -3140,8 +3131,6 @@ void Data::write(FILE *fp, FILE *fp2)
}
if (improper_style) {
- double PI = 3.1415926; // convert back to degrees
-
if ((strcmp(improper_style,"none") != 0) &&
(strcmp(improper_style,"hybrid") != 0))
fprintf(fp,"\nImproper Coeffs\n\n");
@@ -3191,7 +3180,7 @@ void Data::write(FILE *fp, FILE *fp2)
if (style_dipole) write_atom_dipole(fp,i,ix,iy,iz);
if (style_ellipsoid) write_atom_ellipsoid(fp,i,ix,iy,iz);
if (style_full) write_atom_full(fp,i,ix,iy,iz);
- if (style_granular) write_atom_granular(fp,i,ix,iy,iz);
+ if (style_sphere) write_atom_sphere(fp,i,ix,iy,iz);
if (style_molecular) write_atom_molecular(fp,i,ix,iy,iz);
if (style_peri) write_atom_peri(fp,i,ix,iy,iz);
fprintf(fp,"\n");
@@ -3207,7 +3196,7 @@ void Data::write(FILE *fp, FILE *fp2)
if (k == style_dipole) write_atom_dipole_extra(fp,i);
if (k == style_ellipsoid) write_atom_ellipsoid_extra(fp,i);
if (k == style_full) write_atom_full_extra(fp,i);
- if (k == style_granular) write_atom_granular_extra(fp,i);
+ if (k == style_sphere) write_atom_sphere_extra(fp,i);
if (k == style_molecular) write_atom_molecular_extra(fp,i);
if (k == style_peri) write_atom_peri_extra(fp,i);
}
@@ -3228,7 +3217,7 @@ void Data::write(FILE *fp, FILE *fp2)
if (style_dipole) write_vel_dipole(fp,i);
if (style_ellipsoid) write_vel_ellipsoid(fp,i);
if (style_full) write_vel_full(fp,i);
- if (style_granular) write_vel_granular(fp,i);
+ if (style_sphere) write_vel_sphere(fp,i);
if (style_molecular) write_vel_molecular(fp,i);
if (style_peri) write_vel_peri(fp,i);
fprintf(fp,"\n");
@@ -3243,7 +3232,7 @@ void Data::write(FILE *fp, FILE *fp2)
if (k == style_dipole) write_vel_dipole_extra(fp,i);
if (k == style_ellipsoid) write_vel_ellipsoid_extra(fp,i);
if (k == style_full) write_vel_full_extra(fp,i);
- if (k == style_granular) write_vel_granular_extra(fp,i);
+ if (k == style_sphere) write_vel_sphere_extra(fp,i);
if (k == style_molecular) write_vel_molecular_extra(fp,i);
if (k == style_peri) write_vel_peri_extra(fp,i);
}
@@ -3314,14 +3303,15 @@ void Data::write_atom_charge(FILE *fp, int i, int ix, int iy, int iz)
void Data::write_atom_dipole(FILE *fp, int i, int ix, int iy, int iz)
{
fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d",
- tag[i],type[i],q[i],x[i],y[i],z[i],mux[i],muy[i],muz[i],ix,iy,iz);
+ tag[i],type[i],q[i],x[i],y[i],z[i],
+ mux[i],muy[i],muz[i],ix,iy,iz);
}
void Data::write_atom_ellipsoid(FILE *fp, int i, int ix, int iy, int iz)
{
- fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d",
- tag[i],type[i],x[i],y[i],z[i],
- quatw[i],quati[i],quatj[i],quatk[i],ix,iy,iz);
+ fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d",
+ tag[i],type[i],shapex[i],shapey[i],shapez[i],density[i],
+ x[i],y[i],z[i],quatw[i],quati[i],quatj[i],quatk[i],ix,iy,iz);
}
void Data::write_atom_full(FILE *fp, int i, int ix, int iy, int iz)
@@ -3330,7 +3320,7 @@ void Data::write_atom_full(FILE *fp, int i, int ix, int iy, int iz)
tag[i],molecule[i],type[i],q[i],x[i],y[i],z[i],ix,iy,iz);
}
-void Data::write_atom_granular(FILE *fp, int i, int ix, int iy, int iz)
+void Data::write_atom_sphere(FILE *fp, int i, int ix, int iy, int iz)
{
fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d",
tag[i],type[i],2.0*radius[i],density[i],x[i],y[i],z[i],ix,iy,iz);
@@ -3345,7 +3335,7 @@ void Data::write_atom_molecular(FILE *fp, int i, int ix, int iy, int iz)
void Data::write_atom_peri(FILE *fp, int i, int ix, int iy, int iz)
{
fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d",
- tag[i],type[i],vfrac[i],density[i],rmass[i],x[i],y[i],z[i],ix,iy,iz);
+ tag[i],type[i],vfrac[i],rmass[i],x[i],y[i],z[i],ix,iy,iz);
}
// ---------------------------------------------------------------------
@@ -3377,7 +3367,9 @@ void Data::write_atom_dipole_extra(FILE *fp, int i)
void Data::write_atom_ellipsoid_extra(FILE *fp, int i)
{
- fprintf(fp," %-1.16e %-1.16e %-1.16e %-1.16e",quatw[i],quati[i],quatj[i],quatk[i]);
+ fprintf(fp," %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e",
+ shapex[i],shapey[i],shapez[i],density[i],
+ quatw[i],quati[i],quatj[i],quatk[i]);
}
void Data::write_atom_full_extra(FILE *fp, int i)
@@ -3385,7 +3377,7 @@ void Data::write_atom_full_extra(FILE *fp, int i)
fprintf(fp," %d %-1.16e",molecule[i],q[i]);
}
-void Data::write_atom_granular_extra(FILE *fp, int i)
+void Data::write_atom_sphere_extra(FILE *fp, int i)
{
fprintf(fp," %-1.16e %-1.16e",2.0*radius[i],density[i]);
}
@@ -3397,7 +3389,7 @@ void Data::write_atom_molecular_extra(FILE *fp, int i)
void Data::write_atom_peri_extra(FILE *fp, int i)
{
- fprintf(fp," %-1.16e %-1.16e %-1.16e",vfrac[i],density[i],rmass[i]);
+ fprintf(fp," %-1.16e %-1.16e %-1.16e",vfrac[i],rmass[i]);
}
// ---------------------------------------------------------------------
@@ -3441,7 +3433,7 @@ void Data::write_vel_full(FILE *fp, int i)
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e",tag[i],vx[i],vy[i],vz[i]);
}
-void Data::write_vel_granular(FILE *fp, int i)
+void Data::write_vel_sphere(FILE *fp, int i)
{
fprintf(fp,"%d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e",
tag[i],vx[i],vy[i],vz[i],omegax[i],omegay[i],omegaz[i]);
@@ -3475,7 +3467,7 @@ void Data::write_vel_ellipsoid_extra(FILE *fp, int i)
void Data::write_vel_full_extra(FILE *fp, int i) {}
-void Data::write_vel_granular_extra(FILE *fp, int i)
+void Data::write_vel_sphere_extra(FILE *fp, int i)
{
fprintf(fp," %-1.16e %-1.16e %-1.16e",omegax[i],omegay[i],omegaz[i]);
}