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Adding compatability with MC fixes, set_array to property/atom, faster update/special/bonds, single methods, and misc small changes

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This commit is contained in:
Joel Thomas Clemmer
2021-12-08 16:47:42 -07:00
parent f3eac179e6
commit 455cb09cf4
25 changed files with 681 additions and 553 deletions
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13
doc/src/Howto_bpm.rst
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@ -3,7 +3,7 @@ Bonded particle models
The BPM package implements bonded particle models which can be used to
simulate mesoscale solids. Solids are constructed as a collection of
particles which each represent a coarse-grained region of space much
larger than the atomistic scale. Particles within a solid region are
then connected by a network of bonds to provide solid elasticity.
@ -24,7 +24,7 @@ Bonds can be created using a :doc:`read data <read_data>` or
:doc:`create bond <create_bond>` command. Alternatively, a
:doc:`molecule <molecule>` template with bonds can be used with
:doc:`fix deposit <fix_deposit>` or :doc:`fix pour <fix_pour>` to
create solid grains.
create solid grains.
In this implementation, bonds store their reference state when they are
first computed in the setup of the first simulation run. Data is then
@ -47,7 +47,7 @@ this, LAMMPS requires :doc:`newton <newton>` bond off such that all
processors containing an atom know when a bond breaks. Additionally,
one must do either (A) or (B).
(A)
(A)
Use the following special bond settings
@ -64,7 +64,7 @@ charges in BPM models, setting a nonzero coul weight for 1-2 bonds
ensures all bonded neighbors are still included in the neighbor list
in case bonds break between neighbor list builds.
(B)
(B)
Alternatively, one can simply overlay pair interactions such that all
bonded particles also feel pair interactions. This can be accomplished
@ -109,13 +109,14 @@ velocity damping as its sister bond style.
----------
While LAMMPS has many untilites to create and delete bonds, only a
select few are compatible with BPM bond styles. They include:
While LAMMPS has many untilites to create and delete bonds, the
following are currently compatible with BPM bond styles:
* :doc:`create_bonds <create_bonds>`
* :doc:`delete_bonds <delete_bonds>`
* :doc:`fix bond/create <fix_bond_create>`
* :doc:`fix bond/break <fix_bond_break>`
* :doc:`fix bond/swap <fix_bond_swap>`
Note :doc:`bond_create <bond_create>` requires certain special_bonds settings.
To subtract pair interactions, one will need to switch between different

4
doc/src/Howto_broken_bonds.rst
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@ -31,7 +31,9 @@ page.
Bonds can also be broken by fixes which change bond topology, including
:doc:`fix bond/break <fix_bond_break>` and
:doc:`fix bond/react <fix_bond_react>`.
:doc:`fix bond/react <fix_bond_react>`. These fixes will automatically
trigger a rebuild of the neighbor list and update special bond data structures
when bonds are broken.
Note that when bonds are dumped to a file via the :doc:`dump local <dump>` command, bonds with type 0 are not included. The
:doc:`delete_bonds <delete_bonds>` command can also be used to query the

7
doc/src/bond_bpm_rotational.rst
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@ -150,13 +150,18 @@ status of broken bonds or permanently delete them, e.g.:
----------
Restart
Restart and other info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This bond style writes the reference state of each bond to
:doc:`binary restart files <restart>`. Loading a restart file will
properly resume bonds.
The single() function of these pair styles returns 0.0 for the energy
of a pairwise interaction, since energy is not conserved in these
dissipative potentials. It also returns only the normal component of
the pairwise interaction force.
Restrictions
""""""""""""

6
doc/src/bond_bpm_spring.rst
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@ -113,13 +113,17 @@ query the status of broken bonds or permanently delete them, e.g.:
----------
Restart
Restart and other info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This bond style writes the reference state of each bond to
:doc:`binary restart files <restart>`. Loading a restart
file will properly resume bonds.
The single() function of these pair styles returns 0.0 for the energy
of a pairwise interaction, since energy is not conserved in these
dissipative potentials.
Restrictions
""""""""""""

103
examples/bpm/impact/in.bpm.impact.rotational
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@ -1,51 +1,52 @@
units lj
dimension 3
boundary f f f
atom_style sphere/bpm
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
newton on off
comm_modify vel yes cutoff 2.6
lattice fcc 1.0
region box block -25 15 -22 22 -22 22
create_box 1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
region disk cylinder x 0.0 0.0 20.0 -0.5 0.5
create_atoms 1 region disk
group plate region disk
region ball sphere 8.0 0.0 0.0 6.0
create_atoms 1 region ball
group projectile region ball
displace_atoms all random 0.1 0.1 0.1 134598738
neighbor 1.0 bin
pair_style gran/hooke/history 1.0 NULL 0.5 NULL 0.1 1
bond_style bpm/rotational store/local 2 time id1 id2
pair_coeff 1 1
bond_coeff 1 1.0 0.2 0.02 0.02 0.05 0.01 0.01 0.01 0.1 0.02 0.002 0.002
bond_coeff 2 1.0 0.2 0.02 0.02 0.20 0.04 0.04 0.04 0.1 0.02 0.002 0.002
fix 1 all nve/sphere/bpm
fix 2 all store/local 100 3
create_bonds many plate plate 1 0.0 1.5
create_bonds many projectile projectile 2 0.0 1.5
neighbor 0.3 bin
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
velocity projectile set -0.05 0.0 0.0
compute nbond all nbond/atom
compute tbond all reduce sum c_nbond
timestep 0.05
thermo_style custom step ke pe pxx pyy pzz c_tbond
thermo 100
thermo_modify lost ignore lost/bond ignore
#dump 1 all custom 100 atomDump id radius x y z c_nbond
dump 2 all local 100 brokenDump f_2[1] f_2[2] f_2[3]
dump_modify 2 header no
run 7500
units lj
dimension 3
boundary f f f
atom_style sphere/bpm
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
newton on off
comm_modify vel yes cutoff 2.6
lattice fcc 1.0
region box block -25 15 -22 22 -22 22
create_box 1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
region disk cylinder x 0.0 0.0 20.0 -0.5 0.5
create_atoms 1 region disk
group plate region disk
region ball sphere 8.0 0.0 0.0 6.0
create_atoms 1 region ball
group projectile region ball
displace_atoms all random 0.1 0.1 0.1 134598738
neighbor 1.0 bin
pair_style gran/hooke/history 1.0 NULL 0.5 NULL 0.1 1
pair_coeff 1 1
fix 1 all nve/sphere/bpm
fix 2 all store/local 100 3
create_bonds many plate plate 1 0.0 1.5
create_bonds many projectile projectile 2 0.0 1.5
neighbor 0.3 bin
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
bond_style bpm/rotational store/local 2 time id1 id2
bond_coeff 1 1.0 0.2 0.02 0.02 0.05 0.01 0.01 0.01 0.1 0.02 0.002 0.002
bond_coeff 2 1.0 0.2 0.02 0.02 0.20 0.04 0.04 0.04 0.1 0.02 0.002 0.002
velocity projectile set -0.05 0.0 0.0
compute nbond all nbond/atom
compute tbond all reduce sum c_nbond
timestep 0.05
thermo_style custom step ke pe pxx pyy pzz c_tbond
thermo 100
thermo_modify lost ignore lost/bond ignore
#dump 1 all custom 100 atomDump id radius x y z c_nbond
dump 2 all local 100 brokenDump f_2[1] f_2[2] f_2[3]
dump_modify 2 header no
run 7500

107
examples/bpm/impact/in.bpm.impact.spring
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@ -1,53 +1,54 @@
units lj
dimension 3
boundary f f f
atom_style bond
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
newton on off
comm_modify vel yes cutoff 2.6
lattice fcc 1.0
region box block -25 15 -22 22 -22 22
create_box 1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
region disk cylinder x 0.0 0.0 20.0 -0.5 0.5
create_atoms 1 region disk
group plate region disk
region ball sphere 8.0 0.0 0.0 6.0
create_atoms 1 region ball
group projectile region ball
displace_atoms all random 0.1 0.1 0.1 134598738
mass 1 1.0
neighbor 1.0 bin
pair_style bpm/spring
bond_style bpm/spring store/local 2 time id1 id2
pair_coeff 1 1 1.0 1.0 1.0
bond_coeff 1 1.0 0.04 1.0
bond_coeff 2 1.0 0.20 1.0
fix 1 all nve
fix 2 all store/local 100 3
create_bonds many plate plate 1 0.0 1.5
create_bonds many projectile projectile 2 0.0 1.5
neighbor 0.3 bin
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
velocity projectile set -0.05 0.0 0.0
compute nbond all nbond/atom
compute tbond all reduce sum c_nbond
timestep 0.1
thermo_style custom step ke pe pxx pyy pzz c_tbond
thermo 100
thermo_modify lost ignore lost/bond ignore
#dump 1 all custom 100 atomDump id x y z c_nbond
dump 2 all local 100 brokenDump f_2[1] f_2[2] f_2[3]
dump_modify 2 header no
run 7500
units lj
dimension 3
boundary f f f
atom_style bond
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
newton on off
comm_modify vel yes cutoff 2.6
lattice fcc 1.0
region box block -25 15 -22 22 -22 22
create_box 1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
region disk cylinder x 0.0 0.0 20.0 -0.5 0.5
create_atoms 1 region disk
group plate region disk
region ball sphere 8.0 0.0 0.0 6.0
create_atoms 1 region ball
group projectile region ball
displace_atoms all random 0.1 0.1 0.1 134598738
mass 1 1.0
neighbor 1.0 bin
pair_style bpm/spring
pair_coeff 1 1 1.0 1.0 1.0
fix 1 all nve
fix 2 all store/local 100 3
create_bonds many plate plate 1 0.0 1.5
create_bonds many projectile projectile 2 0.0 1.5
neighbor 0.3 bin
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
bond_style bpm/spring store/local 2 time id1 id2
bond_coeff 1 1.0 0.04 1.0
bond_coeff 2 1.0 0.20 1.0
velocity projectile set -0.05 0.0 0.0
compute nbond all nbond/atom
compute tbond all reduce sum c_nbond
timestep 0.1
thermo_style custom step ke pe pxx pyy pzz c_tbond
thermo 100
thermo_modify lost ignore lost/bond ignore
#dump 1 all custom 100 atomDump id x y z c_nbond
dump 2 all local 100 brokenDump f_2[1] f_2[2] f_2[3]
dump_modify 2 header no
run 7500

70
examples/bpm/pour/in.bpm.pour
View File

@ -1,35 +1,35 @@
units lj
dimension 3
boundary m m m
atom_style sphere/bpm
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
newton on off
comm_modify vel yes cutoff 3.3
region box block -15 15 -15 15 0 60.0
create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
molecule my_mol "rect.mol"
region wall_cyl cylinder z 0.0 0.0 10.0 EDGE EDGE side in
region dropzone cylinder z 0.0 0.0 10.0 40.0 50.0 side in
pair_style gran/hertz/history 1.0 NULL 0.5 NULL 0.1 1
bond_style bpm/rotational
pair_coeff 1 1
bond_coeff 1 1.0 0.2 0.01 0.01 2.0 0.4 0.02 0.02 0.2 0.04 0.002 0.002
compute nbond all nbond/atom
compute tbond all reduce sum c_nbond
compute_modify thermo_temp dynamic/dof yes
fix 1 all wall/gran hertz/history 1.0 NULL 0.5 NULL 0.1 1 zplane 0.0 NULL
fix 2 all wall/gran/region hertz/history 1.0 NULL 0.5 NULL 0.1 1 region wall_cyl
fix 3 all gravity 1e-4 vector 0 0 -1
fix 4 all deposit 40 0 1500 712511343 mol my_mol region dropzone near 2.0 vz -0.05 -0.05
fix 5 all nve/sphere/bpm
timestep 0.05
thermo_style custom step ke pe pxx pyy pzz c_tbond
thermo 100
#dump 1 all custom 500 atomDump id radius x y z c_nbond mol
run 100000
units lj
dimension 3
boundary m m m
atom_style sphere/bpm
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
newton on off
comm_modify vel yes cutoff 3.3
region box block -15 15 -15 15 0 60.0
create_box 1 box bond/types 1 extra/bond/per/atom 15 extra/special/per/atom 50
molecule my_mol "rect.mol"
region wall_cyl cylinder z 0.0 0.0 10.0 EDGE EDGE side in
region dropzone cylinder z 0.0 0.0 10.0 40.0 50.0 side in
pair_style gran/hertz/history 1.0 NULL 0.5 NULL 0.1 1
bond_style bpm/rotational
pair_coeff 1 1
bond_coeff 1 1.0 0.2 0.01 0.01 2.0 0.4 0.02 0.02 0.2 0.04 0.002 0.002
compute nbond all nbond/atom
compute tbond all reduce sum c_nbond
compute_modify thermo_temp dynamic/dof yes
fix 1 all wall/gran hertz/history 1.0 NULL 0.5 NULL 0.1 1 zplane 0.0 NULL
fix 2 all wall/gran/region hertz/history 1.0 NULL 0.5 NULL 0.1 1 region wall_cyl
fix 3 all gravity 1e-4 vector 0 0 -1
fix 4 all deposit 40 0 1500 712511343 mol my_mol region dropzone near 2.0 vz -0.05 -0.05
fix 5 all nve/sphere/bpm
timestep 0.05
thermo_style custom step ke pe pxx pyy pzz c_tbond
thermo 100
#dump 1 all custom 500 atomDump id radius x y z c_nbond mol
run 100000

2
src/.gitignore vendored
View File

@ -265,8 +265,6 @@
/compute_nbond_atom.h
/fix_nve_sphere_bpm.cpp
/fix_nve_sphere_bpm.h
/fix_update_special_bonds.cpp
/fix_update_special_bonds.h
/pair_bpm_spring.cpp
/pair_bpm_spring.h

47
src/BPM/bond_bpm.cpp
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@ -25,6 +25,9 @@
#include "modify.h"
#include "update.h"
#include <string>
#include <vector>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
@ -49,7 +52,7 @@ BondBPM::BondBPM(LAMMPS *lmp) : Bond(lmp)
// create dummy fix as placeholder for FixUpdateSpecialBonds
// this is so final order of Modify:fix will conform to input script
id_fix_dummy = utils::strdup("BPM_DUMMY");
id_fix_dummy = utils::strdup("BPM_DUMMY" + std::to_string(instance_me));
modify->add_fix(fmt::format("{} all DUMMY ", id_fix_dummy));
}
@ -58,14 +61,16 @@ BondBPM::BondBPM(LAMMPS *lmp) : Bond(lmp)
BondBPM::~BondBPM()
{
delete [] pack_choice;
delete [] id_fix_store_local;
delete [] id_fix_prop_atom;
if (id_fix_dummy) modify->delete_fix(id_fix_dummy);
if (id_fix_update) modify->delete_fix(id_fix_update);
if (id_fix_store_local) modify->delete_fix(id_fix_store_local);
if (id_fix_prop_atom) modify->delete_fix(id_fix_prop_atom);
delete [] id_fix_dummy;
delete [] id_fix_update;
delete [] id_fix_store_local;
delete [] id_fix_prop_atom;
memory->destroy(output_data);
}
@ -110,7 +115,7 @@ void BondBPM::init_style()
error->all(FLERR,"Without overlay/pair, BPM bond sytles requires special Coulomb weights = 1,1,1");
if (id_fix_dummy) {
id_fix_update = utils::strdup("BPM_update_special_bonds");
id_fix_update = utils::strdup("BPM_update_special_bonds" + std::to_string(instance_me));
fix_update_special_bonds = (FixUpdateSpecialBonds *) modify->replace_fix(id_fix_dummy,
fmt::format("{} all UPDATE_SPECIAL_BONDS", id_fix_update),1);
delete [] id_fix_dummy;
@ -141,11 +146,14 @@ void BondBPM::init_style()
void BondBPM::settings(int narg, char **arg)
{
leftover_args.clear();
int local_freq;
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg], "store/local") == 0) {
id_fix_store_local = utils::strdup(arg[iarg+1]);
nvalues = 0;
local_freq = utils::inumeric(FLERR, arg[iarg+1], false, lmp);
pack_choice = new FnPtrPack[narg - iarg - 1];
iarg += 2;
while (iarg < narg) {
@ -179,31 +187,44 @@ void BondBPM::settings(int narg, char **arg)
overlay_flag = 1;
iarg ++;
} else {
error->all(FLERR, "Illegal pair_style command");
leftover_args.push_back(iarg);
iarg ++;
}
}
if (id_fix_store_local) {
if (nvalues != 0 && !id_fix_store_local) {
//Todo, assign ID and create fix id_fix_store_local = utils::strdup(arg[iarg+1]);
if (nvalues == 0) error->all(FLERR,
"Bond style bpm/rotational must include at least one value to output");
memory->create(output_data, nvalues, "bond/bpm:output_data");
// Use store property to save reference positions as it can transfer to ghost atoms
// This won't work for instances where bonds are added (e.g. fix pour) but in those cases
// a reference state isn't well defined
if (prop_atom_flag == 1) {
id_fix_prop_atom = utils::strdup("BPM_property_atom");
id_fix_prop_atom = utils::strdup("BPM_property_atom" + std::to_string(instance_me));
int ifix = modify->find_fix(id_fix_prop_atom);
char *x_ref_id = utils::strdup("BPM_X_REF" + std::to_string(instance_me));
char *y_ref_id = utils::strdup("BPM_Y_REF" + std::to_string(instance_me));
char *z_ref_id = utils::strdup("BPM_Z_REF" + std::to_string(instance_me));
if (ifix < 0) {
modify->add_fix(fmt::format("{} all property/atom "
"d_BPM_X_REF d_BPM_Y_REF d_BPM_Z_REF ghost yes", id_fix_prop_atom));
modify->add_fix(fmt::format("{} all property/atom {} {} {} ghost yes",
id_fix_prop_atom, x_ref_id, y_ref_id, z_ref_id));
ifix = modify->find_fix(id_fix_prop_atom);
}
int type_flag;
int col_flag;
index_x_ref = atom->find_custom("BPM_X_REF", type_flag, col_flag);
index_y_ref = atom->find_custom("BPM_Y_REF", type_flag, col_flag);
index_z_ref = atom->find_custom("BPM_Z_REF", type_flag, col_flag);
index_x_ref = atom->find_custom(x_ref_id, type_flag, col_flag);
index_y_ref = atom->find_custom(y_ref_id, type_flag, col_flag);
index_z_ref = atom->find_custom(z_ref_id, type_flag, col_flag);
delete [] x_ref_id;
delete [] y_ref_id;
delete [] z_ref_id;
if (modify->fix[ifix]->restart_reset) {
modify->fix[ifix]->restart_reset = 0;

4
src/BPM/bond_bpm.h
View File

@ -16,6 +16,8 @@
#include "bond.h"
#include <vector>
namespace LAMMPS_NS {
class BondBPM : public Bond {
@ -36,6 +38,8 @@ class BondBPM : public Bond {
double r0_max_estimate;
double max_stretch;
std::vector<int> leftover_args;
char *id_fix_dummy, *id_fix_update;
char *id_fix_store_local, *id_fix_prop_atom;
class FixStoreLocal *fix_store_local;

577
src/BPM/bond_bpm_rotational.cpp
View File

@ -176,6 +176,270 @@ void BondBPMRotational::store_data()
fix_bond_history->post_neighbor();
}
/* ----------------------------------------------------------------------
Calculate forces using formulation in:
1) Y. Wang Acta Geotechnica 2009
2) P. Mora & Y. Wang Advances in Geomcomputing 2009
---------------------------------------------------------------------- */
double BondBPMRotational::elastic_forces(int i1, int i2, int type, double& Fr,
double r_mag, double r0_mag, double r_mag_inv, double* rhat, double* r,
double* r0, double* force1on2, double* torque1on2, double* torque2on1)
{
int m;
double breaking, temp, r0_dot_rb, c, gamma;
double psi, theta, cos_phi, sin_phi;
double mag_in_plane, mag_out_plane;
double Fs_mag, Tt_mag, Tb_mag;
double q1[4], q2[4];
double q2inv[4], mq[4], mqinv[4], qp21[4], q21[4], qtmp[4];
double rb[3], rb_x_r0[3], s[3], t[3];
double Fs[3], Fsp[3], F_rot[3], Ftmp[3];
double Ts[3], Tb[3], Tt[3], Tbp[3], Ttp[3], Tsp[3], T_rot[3], Ttmp[3];
double **quat = atom->quat;
q1[0] = quat[i1][0];
q1[1] = quat[i1][1];
q1[2] = quat[i1][2];
q1[3] = quat[i1][3];
q2[0] = quat[i2][0];
q2[1] = quat[i2][1];
q2[2] = quat[i2][2];
q2[3] = quat[i2][3];
// Calculate normal forces, rb = bond vector in particle 1's frame
MathExtra::qconjugate(q2, q2inv);
MathExtra::quatrotvec(q2inv, r, rb);
Fr = Kr[type]*(r_mag - r0_mag);
MathExtra::scale3(Fr*r_mag_inv, rb, F_rot);
// Calculate forces due to tangential displacements (no rotation)
r0_dot_rb = dot3(r0, rb);
c = r0_dot_rb*r_mag_inv/r0_mag;
gamma = acos_limit(c);
MathExtra::cross3(rb, r0, rb_x_r0);
MathExtra::cross3(rb, rb_x_r0, s);
MathExtra::norm3(s);
MathExtra::scale3(Ks[type]*r_mag*gamma, s, Fs);
// Calculate torque due to tangential displacements
MathExtra::cross3(r0, rb, t);
MathExtra::norm3(t);
MathExtra::scale3(0.5*r_mag*Ks[type]*r_mag*gamma, t, Ts);
// Relative rotation force/torque
// Use representation of X'Y'Z' rotations from Wang, Mora 2009
temp = r_mag + rb[2];
if (temp < 0.0) temp = 0.0;
mq[0] = sqrt(2)*0.5*sqrt(temp*r_mag_inv);
temp = sqrt(rb[0]*rb[0]+rb[1]*rb[1]);
if (temp != 0.0) {
mq[1] = -sqrt(2)*0.5/temp;
temp = r_mag - rb[2];
if (temp < 0.0) temp = 0.0;
mq[1] *= sqrt(temp*r_mag_inv);
mq[2] = -mq[1];
mq[1] *= rb[1];
mq[2] *= rb[0];
} else {
// If aligned along z axis, x,y terms zero (r_mag-rb[2] = 0)
mq[1] = 0.0;
mq[2] = 0.0;
}
mq[3] = 0.0;
// qp21 = opposite of r^\circ_21 in Wang
// q21 = opposite of r_21 in Wang
MathExtra::quatquat(q2inv, q1, qp21);
MathExtra::qconjugate(mq, mqinv);
MathExtra::quatquat(mqinv,qp21,qtmp);
MathExtra::quatquat(qtmp,mq,q21);
temp = sqrt(q21[0]*q21[0] + q21[3]*q21[3]);
if (temp != 0.0) {
c = q21[0]/temp;
psi = 2.0*acos_limit(c);
} else {
c = 0.0;
psi = 0.0;
}
// Map negative rotations
if (q21[3] < 0.0) // sin = q21[3]/temp
psi = -psi;
if (q21[3] == 0.0)
psi = 0.0;
c = q21[0]*q21[0] - q21[1]*q21[1] - q21[2]*q21[2] + q21[3]*q21[3];
theta = acos_limit(c);
// Separately calculte magnitude of quaternion in x-y and out of x-y planes
// to avoid dividing by zero
mag_out_plane = (q21[0]*q21[0] + q21[3]*q21[3]);
mag_in_plane = (q21[1]*q21[1] + q21[2]*q21[2]);
if (mag_in_plane == 0.0) {
// No rotation => no bending/shear torque or extra shear force
// achieve by setting cos/sin = 0
cos_phi = 0.0;
sin_phi = 0.0;
} else if (mag_out_plane == 0.0) {
// Calculate angle in plane
cos_phi = q21[2]/sqrt(mag_in_plane);
sin_phi = -q21[1]/sqrt(mag_in_plane);
} else {
// Default equations in Mora, Wang 2009
cos_phi = q21[1]*q21[3] + q21[0]*q21[2];
sin_phi = q21[2]*q21[3] - q21[0]*q21[1];
cos_phi /= sqrt(mag_out_plane*mag_in_plane);
sin_phi /= sqrt(mag_out_plane*mag_in_plane);
}
Tbp[0] = -Kb[type]*theta*sin_phi;
Tbp[1] = Kb[type]*theta*cos_phi;
Tbp[2] = 0.0;
Ttp[0] = 0.0;
Ttp[1] = 0.0;
Ttp[2] = Kt[type]*psi;
Fsp[0] = -0.5*Ks[type]*r_mag*theta*cos_phi;
Fsp[1] = -0.5*Ks[type]*r_mag*theta*sin_phi;
Fsp[2] = 0.0;
Tsp[0] = 0.25*Ks[type]*r_mag*r_mag*theta*sin_phi;
Tsp[1] = -0.25*Ks[type]*r_mag*r_mag*theta*cos_phi;
Tsp[2] = 0.0;
// Rotate forces/torques back to 1st particle's frame
MathExtra::quatrotvec(mq, Fsp, Ftmp);
MathExtra::quatrotvec(mq, Tsp, Ttmp);
for (m = 0; m < 3; m++) {
Fs[m] += Ftmp[m];
Ts[m] += Ttmp[m];
}
MathExtra::quatrotvec(mq, Tbp, Tb);
MathExtra::quatrotvec(mq, Ttp, Tt);
// Sum forces and calculate magnitudes
F_rot[0] += Fs[0];
F_rot[1] += Fs[1];
F_rot[2] += Fs[2];
MathExtra::quatrotvec(q2, F_rot, force1on2);
T_rot[0] = Ts[0] + Tt[0] + Tb[0];
T_rot[1] = Ts[1] + Tt[1] + Tb[1];
T_rot[2] = Ts[2] + Tt[2] + Tb[2];
MathExtra::quatrotvec(q2, T_rot, torque1on2);
T_rot[0] = Ts[0] - Tt[0] - Tb[0];
T_rot[1] = Ts[1] - Tt[1] - Tb[1];
T_rot[2] = Ts[2] - Tt[2] - Tb[2];
MathExtra::quatrotvec(q2, T_rot, torque2on1);
Fs_mag = MathExtra::len3(Fs);
Tt_mag = MathExtra::len3(Tt);
Tb_mag = MathExtra::len3(Tb);
breaking = Fr/Fcr[type] + Fs_mag/Fcs[type] + Tb_mag/Tcb[type] + Tt_mag/Tct[type];
if (breaking < 0.0) breaking = 0.0;
return breaking;
}
/* ----------------------------------------------------------------------
Calculate damping using formulation in
Y. Wang, F. Alonso-Marroquin, W. Guo 2015
Note: n points towards 1 vs pointing towards 2
---------------------------------------------------------------------- */
void BondBPMRotational::damping_forces(int i1, int i2, int type, double& Fr,
double* rhat, double* r, double* force1on2, double* torque1on2,
double* torque2on1)
{
double v1dotr, v2dotr, w1dotr, w2dotr;
double s1[3], s2[3], tdamp[3], tmp[3];
double vn1[3], vn2[3], vt1[3], vt2[3], vroll[3];
double wxn1[3], wxn2[3], wn1[3], wn2[3];
double **v = atom->v;
double **omega = atom->omega;
// Damp normal velocity difference
v1dotr = MathExtra::dot3(v[i1],rhat);
v2dotr = MathExtra::dot3(v[i2],rhat);
MathExtra::scale3(v1dotr, rhat, vn1);
MathExtra::scale3(v2dotr, rhat, vn2);
MathExtra::sub3(vn1, vn2, tmp);
MathExtra::scale3(gnorm[type], tmp);
Fr = MathExtra::lensq3(tmp);
MathExtra::add3(force1on2, tmp, force1on2);
// Damp tangential objective velocities
MathExtra::sub3(v[i1], vn1, vt1);
MathExtra::sub3(v[i2], vn2, vt2);
MathExtra::sub3(vt2, vt1, tmp);
MathExtra::scale3(-0.5, tmp);
MathExtra::cross3(omega[i1], r, s1);
MathExtra::scale3(0.5, s1);
MathExtra::sub3(s1, tmp, s1); // Eq 12
MathExtra::cross3(omega[i2], r, s2);
MathExtra::scale3(-0.5,s2);
MathExtra::add3(s2, tmp, s2); // Eq 13
MathExtra::scale3(-0.5,s2);
MathExtra::sub3(s1, s2, tmp);
MathExtra::scale3(gslide[type], tmp);
MathExtra::add3(force1on2, tmp, force1on2);
// Apply corresponding torque
MathExtra::cross3(r,tmp,tdamp);
MathExtra::scale3(-0.5, tdamp); // 0.5*r points from particle 2 to midpoint
MathExtra::add3(torque1on2, tdamp, torque1on2);
MathExtra::add3(torque2on1, tdamp, torque2on1);
// Damp rolling
MathExtra::cross3(omega[i1], rhat, wxn1);
MathExtra::cross3(omega[i2], rhat, wxn2);
MathExtra::sub3(wxn1, wxn2, vroll); // Eq. 31
MathExtra::cross3(r, vroll, tdamp);
MathExtra::scale3(0.5*groll[type], tdamp);
MathExtra::add3(torque1on2, tdamp, torque1on2);
MathExtra::scale3(-1.0, tdamp);
MathExtra::add3(torque2on1, tdamp, torque2on1);
// Damp twist
w1dotr = MathExtra::dot3(omega[i1],rhat);
w2dotr = MathExtra::dot3(omega[i2],rhat);
MathExtra::scale3(w1dotr, rhat, wn1);
MathExtra::scale3(w2dotr, rhat, wn2);
MathExtra::sub3(wn1, wn2, tdamp); // Eq. 38
MathExtra::scale3(0.5*gtwist[type], tdamp);
MathExtra::add3(torque1on2, tdamp, torque1on2);
MathExtra::scale3(-1.0, tdamp);
MathExtra::add3(torque2on1, tdamp, torque2on1);
}
/* ---------------------------------------------------------------------- */
void BondBPMRotational::compute(int eflag, int vflag)
@ -186,32 +450,18 @@ void BondBPMRotational::compute(int eflag, int vflag)
store_data();
}
int i1,i2,itmp,m,n,type,itype,jtype;
double q1[4], q2[4], r[3], r0[3];
double rsq, r0_mag, r_mag, r_mag_inv, Fr, Fs_mag;
double Tt_mag, Tb_mag, breaking, smooth;
int i1,i2,itmp,n,type;
double r[3], r0[3], rhat[3];
double delx, dely, delz, rsq, r0_mag, r_mag, r_mag_inv;
double Fr, breaking, smooth;
double force1on2[3], torque1on2[3], torque2on1[3];
double rhat[3], wn1[3], wn2[3], wxn1[3], wxn2[3], vroll[3];
double w1dotr, w2dotr, v1dotr, v2dotr;
double vn1[3], vn2[3], vt1[3], vt2[3], tmp[3], s1[3], s2[3], tdamp[3];
double tor1, tor2, tor3, fs1, fs2, fs3;
double q2inv[4], rb[3], rb_x_r0[3], s[3], t[3], Fs[3];
double q21[4], qp21[4], Tbp[3], Ttp[3];
double Tsp[3], Fsp[3], Tt[3], Tb[3], Ts[3], F_rot[3], T_rot[3];
double mq[4], mqinv[4], Ttmp[3], Ftmp[3], qtmp[4];
double r0_dot_rb, gamma, c, psi, theta, sin_phi, cos_phi, temp;
double mag_in_plane, mag_out_plane;
ev_init(eflag,vflag);
double **x = atom->x;
double **v = atom->v;
double **omega = atom->omega;
double **f = atom->f;
double **torque = atom->torque;
double *radius = atom->radius;
double **quat = atom->quat;
tagint *tag = atom->tag;
int **bondlist = neighbor->bondlist;
int nbondlist = neighbor->nbondlist;
@ -249,16 +499,6 @@ void BondBPMRotational::compute(int eflag, int vflag)
r0[2] = bondstore[n][3];
MathExtra::scale3(r0_mag, r0);
q1[0] = quat[i1][0];
q1[1] = quat[i1][1];
q1[2] = quat[i1][2];
q1[3] = quat[i1][3];
q2[0] = quat[i2][0];
q2[1] = quat[i2][1];
q2[2] = quat[i2][2];
q2[3] = quat[i2][3];
// Note this is the reverse of Mora & Wang
MathExtra::sub3(x[i1], x[i2], r);
@ -268,160 +508,11 @@ void BondBPMRotational::compute(int eflag, int vflag)
MathExtra::scale3(r_mag_inv, r, rhat);
// ------------------------------------------------------//
// Calculate forces using formulation in:
// 1) Y. Wang Acta Geotechnica 2009
// 2) P. Mora & Y. Wang Advances in Geomcomputing 2009
// Calculate forces, check if bond breaks
// ------------------------------------------------------//
// Calculate normal forces, rb = bond vector in particle 1's frame
MathExtra::qconjugate(q2, q2inv);
MathExtra::quatrotvec(q2inv, r, rb);
Fr = Kr[type]*(r_mag - r0_mag);
MathExtra::scale3(Fr*r_mag_inv, rb, F_rot);
// Calculate forces due to tangential displacements (no rotation)
r0_dot_rb = dot3(r0, rb);
c = r0_dot_rb*r_mag_inv/r0_mag;
gamma = acos_limit(c);
MathExtra::cross3(rb, r0, rb_x_r0);
MathExtra::cross3(rb, rb_x_r0, s);
MathExtra::norm3(s);
MathExtra::scale3(Ks[type]*r_mag*gamma, s, Fs);
// Calculate torque due to tangential displacements
MathExtra::cross3(r0, rb, t);
MathExtra::norm3(t);
MathExtra::scale3(0.5*r_mag*Ks[type]*r_mag*gamma, t, Ts);
// Relative rotation force/torque
// Use representation of X'Y'Z' rotations from Wang, Mora 2009
temp = r_mag + rb[2];
if (temp < 0.0) temp = 0.0;
mq[0] = sqrt(2)*0.5*sqrt(temp*r_mag_inv);
temp = sqrt(rb[0]*rb[0]+rb[1]*rb[1]);
if (temp != 0.0) {
mq[1] = -sqrt(2)*0.5/temp;
temp = r_mag - rb[2];
if (temp < 0.0) temp = 0.0;
mq[1] *= sqrt(temp*r_mag_inv);
mq[2] = -mq[1];
mq[1] *= rb[1];
mq[2] *= rb[0];
} else {
// If aligned along z axis, x,y terms zero (r_mag-rb[2] = 0)
mq[1] = 0.0;
mq[2] = 0.0;
}
mq[3] = 0.0;
// qp21 = opposite of r^\circ_21 in Wang
// q21 = opposite of r_21 in Wang
MathExtra::quatquat(q2inv, q1, qp21);
MathExtra::qconjugate(mq, mqinv);
MathExtra::quatquat(mqinv,qp21,qtmp);
MathExtra::quatquat(qtmp,mq,q21);
temp = sqrt(q21[0]*q21[0] + q21[3]*q21[3]);
if (temp != 0.0) {
c = q21[0]/temp;
psi = 2.0*acos_limit(c);
} else {
c = 0.0;
psi = 0.0;
}
// Map negative rotations
if (q21[3] < 0.0) // sin = q21[3]/temp
psi = -psi;
if (q21[3] == 0.0)
psi = 0.0;
c = q21[0]*q21[0] - q21[1]*q21[1] - q21[2]*q21[2] + q21[3]*q21[3];
theta = acos_limit(c);
// Separately calculte magnitude of quaternion in x-y and out of x-y planes
// to avoid dividing by zero
mag_out_plane = (q21[0]*q21[0] + q21[3]*q21[3]);
mag_in_plane = (q21[1]*q21[1] + q21[2]*q21[2]);
if (mag_in_plane == 0.0) {
// No rotation => no bending/shear torque or extra shear force
// achieve by setting cos/sin = 0
cos_phi = 0.0;
sin_phi = 0.0;
} else if (mag_out_plane == 0.0) {
// Calculate angle in plane
cos_phi = q21[2]/sqrt(mag_in_plane);
sin_phi = -q21[1]/sqrt(mag_in_plane);
} else {
// Default equations in Mora, Wang 2009
cos_phi = q21[1]*q21[3] + q21[0]*q21[2];
sin_phi = q21[2]*q21[3] - q21[0]*q21[1];
cos_phi /= sqrt(mag_out_plane*mag_in_plane);
sin_phi /= sqrt(mag_out_plane*mag_in_plane);
}
Tbp[0] = -Kb[type]*theta*sin_phi;
Tbp[1] = Kb[type]*theta*cos_phi;
Tbp[2] = 0.0;
Ttp[0] = 0.0;
Ttp[1] = 0.0;
Ttp[2] = Kt[type]*psi;
Fsp[0] = -0.5*Ks[type]*r_mag*theta*cos_phi;
Fsp[1] = -0.5*Ks[type]*r_mag*theta*sin_phi;
Fsp[2] = 0.0;
Tsp[0] = 0.25*Ks[type]*r_mag*r_mag*theta*sin_phi;
Tsp[1] = -0.25*Ks[type]*r_mag*r_mag*theta*cos_phi;
Tsp[2] = 0.0;
// Rotate forces/torques back to 1st particle's frame
MathExtra::quatrotvec(mq, Fsp, Ftmp);
MathExtra::quatrotvec(mq, Tsp, Ttmp);
for (m = 0; m < 3; m++) {
Fs[m] += Ftmp[m];
Ts[m] += Ttmp[m];
}
MathExtra::quatrotvec(mq, Tbp, Tb);
MathExtra::quatrotvec(mq, Ttp, Tt);
// Sum forces and calculate magnitudes
F_rot[0] += Fs[0];
F_rot[1] += Fs[1];
F_rot[2] += Fs[2];
MathExtra::quatrotvec(q2, F_rot, force1on2);
T_rot[0] = Ts[0] + Tt[0] + Tb[0];
T_rot[1] = Ts[1] + Tt[1] + Tb[1];
T_rot[2] = Ts[2] + Tt[2] + Tb[2];
MathExtra::quatrotvec(q2, T_rot, torque1on2);
T_rot[0] = Ts[0] - Tt[0] - Tb[0];
T_rot[1] = Ts[1] - Tt[1] - Tb[1];
T_rot[2] = Ts[2] - Tt[2] - Tb[2];
MathExtra::quatrotvec(q2, T_rot, torque2on1);
Fs_mag = MathExtra::len3(Fs);
Tt_mag = MathExtra::len3(Tt);
Tb_mag = MathExtra::len3(Tb);
// ------------------------------------------------------//
// Check if bond breaks
// ------------------------------------------------------//
breaking = Fr/Fcr[type] + Fs_mag/Fcs[type] + Tb_mag/Tcb[type] + Tt_mag/Tct[type];
if (breaking < 0.0) breaking = 0.0;
breaking = elastic_forces(i1, i2, type, Fr, r_mag, r0_mag, r_mag_inv,
rhat, r, r0, force1on2, torque1on2, torque2on1);
if (breaking >= 1.0) {
bondlist[n][2] = 0;
@ -429,76 +520,11 @@ void BondBPMRotational::compute(int eflag, int vflag)
continue;
}
damping_forces(i1, i2, type, Fr, rhat, r, force1on2, torque1on2, torque2on1);
smooth = breaking*breaking;
smooth = 1.0 - smooth*smooth;
// ------------------------------------------------------//
// Calculate damping using formulation in
// Y. Wang, F. Alonso-Marroquin, W. Guo 2015
// ------------------------------------------------------//
// Note: n points towards 1 vs pointing towards 2
// Damp normal velocity difference
v1dotr = MathExtra::dot3(v[i1],rhat);
v2dotr = MathExtra::dot3(v[i2],rhat);
MathExtra::scale3(v1dotr, rhat, vn1);
MathExtra::scale3(v2dotr, rhat, vn2);
MathExtra::sub3(vn1, vn2, tmp);
MathExtra::scale3(gnorm[type], tmp);
MathExtra::add3(force1on2, tmp, force1on2);
// Damp tangential objective velocities
MathExtra::sub3(v[i1], vn1, vt1);
MathExtra::sub3(v[i2], vn2, vt2);
MathExtra::sub3(vt2, vt1, tmp);
MathExtra::scale3(-0.5, tmp);
MathExtra::cross3(omega[i1], r, s1);
MathExtra::scale3(0.5, s1);
MathExtra::sub3(s1, tmp, s1); // Eq 12
MathExtra::cross3(omega[i2], r, s2);
MathExtra::scale3(-0.5,s2);
MathExtra::add3(s2, tmp, s2); // Eq 13
MathExtra::scale3(-0.5,s2);
MathExtra::sub3(s1, s2, tmp);
MathExtra::scale3(gslide[type], tmp);
MathExtra::add3(force1on2, tmp, force1on2);
// Apply corresponding torque
MathExtra::cross3(r,tmp,tdamp);
MathExtra::scale3(-0.5, tdamp); // 0.5*r points from particle 2 to midpoint
MathExtra::add3(torque1on2, tdamp, torque1on2);
MathExtra::add3(torque2on1, tdamp, torque2on1);
// Damp rolling
MathExtra::cross3(omega[i1], rhat, wxn1);
MathExtra::cross3(omega[i2], rhat, wxn2);
MathExtra::sub3(wxn1, wxn2, vroll); // Eq. 31
MathExtra::cross3(r, vroll, tdamp);
MathExtra::scale3(0.5*groll[type], tdamp);
MathExtra::add3(torque1on2, tdamp, torque1on2);
MathExtra::scale3(-1.0, tdamp);
MathExtra::add3(torque2on1, tdamp, torque2on1);
// Damp twist
w1dotr = MathExtra::dot3(omega[i1],rhat);
w2dotr = MathExtra::dot3(omega[i2],rhat);
MathExtra::scale3(w1dotr, rhat, wn1);
MathExtra::scale3(w2dotr, rhat, wn2);
MathExtra::sub3(wn1, wn2, tdamp); // Eq. 38
MathExtra::scale3(0.5*gtwist[type], tdamp);
MathExtra::add3(torque1on2, tdamp, torque1on2);
MathExtra::scale3(-1.0, tdamp);
MathExtra::add3(torque2on1, tdamp, torque2on1);
// ------------------------------------------------------//
// Apply forces and torques to particles
// ------------------------------------------------------//
@ -617,7 +643,18 @@ void BondBPMRotational::init_style()
if (!fix_bond_history)
fix_bond_history = (FixBondHistory *) modify->add_fix(
"BOND_HISTORY_BPM_ROTATIONAL all BOND_HISTORY 0 4");
"HISTORY_BPM_ROTATIONAL" + std::to_string(instance_me) + " all BOND_HISTORY 0 4");
}
/* ---------------------------------------------------------------------- */
void BondBPMRotational::settings(int narg, char **arg)
{
BondBPM::settings(narg, arg);
for (int iarg : leftover_args) {
error->all(FLERR, "Illegal bond_style command");
}
}
/* ----------------------------------------------------------------------
@ -698,10 +735,42 @@ double BondBPMRotational::single(int type, double rsq, int i, int j,
// Not yet enabled
if (type <= 0) return 0.0;
//double r0;
//for (int n = 0; n < atom->num_bond[i]; n ++) {
// if (atom->bond_atom[i][n] == atom->tag[j]) {
// r0 = fix_bond_history->get_atom_value(i, n, 0);
// }
//}
int itmp;
if (atom->tag[j] < atom->tag[i]) {
itmp = i;
i = j;
j = itmp;
}
double r0_mag, r_mag, r_mag_inv;
double r0[3], r[3], rhat[3];
for (int n = 0; n < atom->num_bond[i]; n ++) {
if (atom->bond_atom[i][n] == atom->tag[j]) {
r0_mag = fix_bond_history->get_atom_value(i, n, 0);
r0[0] = fix_bond_history->get_atom_value(i, n, 1);
r0[1] = fix_bond_history->get_atom_value(i, n, 2);
r0[2] = fix_bond_history->get_atom_value(i, n, 3);
}
}
double **x = atom->x;
MathExtra::scale3(r0_mag, r0);
MathExtra::sub3(x[i], x[j], r);
r_mag = sqrt(rsq);
r_mag_inv = 1.0/r_mag;
MathExtra::scale3(r_mag_inv, r, rhat);
double breaking, smooth, Fr;
double force1on2[3], torque1on2[3], torque2on1[3];
breaking = elastic_forces(i, j, type, Fr, r_mag, r0_mag, r_mag_inv,
rhat, r, r0, force1on2, torque1on2, torque2on1);
fforce = Fr;
damping_forces(i, j, type, Fr, rhat, r, force1on2, torque1on2, torque2on1);
fforce += Fr;
smooth = breaking*breaking;
smooth = 1.0 - smooth*smooth;
fforce *= smooth;
return 0.0;
}

6
src/BPM/bond_bpm_rotational.h
View File

@ -31,6 +31,7 @@ class BondBPMRotational : public BondBPM {
virtual void compute(int, int);
void coeff(int, char **);
void init_style();
void settings(int, char **);
void write_restart(FILE *);
void read_restart(FILE *);
void write_data(FILE *);
@ -41,6 +42,11 @@ class BondBPMRotational : public BondBPM {
double *Fcr, *Fcs, *Tct, *Tcb;
double acos_limit(double);
double elastic_forces(int, int, int, double &, double, double, double,
double*, double*, double*, double*, double*, double*);
void damping_forces(int, int, int, double &, double*, double*, double*,
double*, double*);
void allocate();
void store_data();
double store_bond(int, int, int);

56
src/BPM/bond_bpm_spring.cpp
View File

@ -136,7 +136,7 @@ void BondBPMSpring::compute(int eflag, int vflag)
int i1,i2,itmp,m,n,type,itype,jtype;
double delx, dely, delz, delvx, delvy, delvz;
double e, rsq, r, r0, rinv, smooth, fbond, ebond, dot;
double e, rsq, r, r0, rinv, smooth, fbond, dot;
ev_init(eflag,vflag);
@ -190,7 +190,6 @@ void BondBPMSpring::compute(int eflag, int vflag)
rinv = 1.0/r;
fbond = k[type]*(r0-r);
if (eflag) ebond = -0.5*fbond*(r0-r);
delvx = v[i1][0] - v[i2][0];
delvy = v[i1][1] - v[i2][1];
@ -218,7 +217,7 @@ void BondBPMSpring::compute(int eflag, int vflag)
f[i2][2] -= delz*fbond;
}
if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz);
if (evflag) ev_tally(i1,i2,nlocal,newton_bond,0.0,fbond,delx,dely,delz);
}
}
@ -280,7 +279,18 @@ void BondBPMSpring::init_style()
if (!fix_bond_history)
fix_bond_history = (FixBondHistory *) modify->add_fix(
"BOND_HISTORY_BPM_SPRING all BOND_HISTORY 0 1");
"HISTORY_BPM_SPRING_" + std::to_string(instance_me) + " all BOND_HISTORY 0 1");
}
/* ---------------------------------------------------------------------- */
void BondBPMSpring::settings(int narg, char **arg)
{
BondBPM::settings(narg, arg);
for (int iarg : leftover_args) {
error->all(FLERR, "Illegal bond_style command");
}
}
/* ----------------------------------------------------------------------
@ -329,13 +339,37 @@ void BondBPMSpring::write_data(FILE *fp)
double BondBPMSpring::single(int type, double rsq, int i, int j,
double &fforce)
{
// Not yet enabled
if (type <= 0) return 0.0;
//double r0;
//for (int n = 0; n < atom->num_bond[i]; n ++) {
// if (atom->bond_atom[i][n] == atom->tag[j]) {
// r0 = fix_bond_history->get_atom_value(i, n, 0);
// }
//}
double r0;
for (int n = 0; n < atom->num_bond[i]; n ++) {
if (atom->bond_atom[i][n] == atom->tag[j]) {
r0 = fix_bond_history->get_atom_value(i, n, 0);
}
}
double r = sqrt(rsq);
double rinv = 1.0/r;
double e = (r - r0)/r0;
fforce = k[type]*(r0-r);
double **x = atom->x;
double **v = atom->v;
double delx = x[i][0] - x[j][0];
double dely = x[i][1] - x[j][1];
double delz = x[i][2] - x[j][2];
double delvx = v[i][0] - v[j][0];
double delvy = v[i][1] - v[j][1];
double delvz = v[i][2] - v[j][2];
double dot = delx*delvx + dely*delvy + delz*delvz;
fforce -= gamma[type]*dot*rinv;
double smooth = (r-r0)/(r0*ecrit[type]);
smooth *= smooth;
smooth *= smooth;
smooth *= smooth;
smooth = 1 - smooth;
fforce *= rinv*smooth;
return 0.0;
}

1
src/BPM/bond_bpm_spring.h
View File

@ -31,6 +31,7 @@ class BondBPMSpring : public BondBPM {
virtual void compute(int, int);
void coeff(int, char **);
void init_style();
void settings(int, char **);
void write_restart(FILE *);
void read_restart(FILE *);
void write_data(FILE *);

7
src/BPM/pair_bpm_spring.cpp
View File

@ -112,7 +112,6 @@ void PairBPMSpring::compute(int eflag, int vflag)
rinv = 1.0/r;
fpair = k[itype][jtype]*(cut[itype][jtype]-r);
if (eflag) evdwl = -0.5 * fpair * (cut[itype][jtype]-r) * factor_lj;
smooth = rsq/cutsq[itype][jtype];
smooth *= smooth;
@ -125,6 +124,7 @@ void PairBPMSpring::compute(int eflag, int vflag)
fpair -= gamma[itype][jtype]*dot*smooth*rinv;
fpair *= factor_lj*rinv;
if (eflag) evdwl = 0.0;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
@ -307,7 +307,7 @@ double PairBPMSpring::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double fpair,philj,r,rinv;
double fpair,r,rinv;
double delx, dely, delz, delvx, delvy, delvz, dot, smooth;
if(rsq > cutsq[itype][jtype]) return 0.0;
@ -319,7 +319,6 @@ double PairBPMSpring::single(int i, int j, int itype, int jtype, double rsq,
rinv = 1.0/r;
fpair = k[itype][jtype]*(cut[itype][jtype]-r);
philj = -0.5*k[itype][jtype]*(cut[itype][jtype]-r)*(cut[itype][jtype]-r);
smooth = rsq/cutsq[itype][jtype];
smooth *= smooth;
@ -336,5 +335,5 @@ double PairBPMSpring::single(int i, int j, int itype, int jtype, double rsq,
fpair *= factor_lj;
fforce = fpair;
return philj;
return 0.0;
}

6
src/bond.cpp
View File

@ -28,6 +28,10 @@ using namespace LAMMPS_NS;
enum{NONE,LINEAR,SPLINE};
// allocate space for static class instance variable and initialize it
int Bond::instance_total = 0;
/* -----------------------------------------------------------------------
set bond contribution to Vdwl energy to 0.0
a particular bond style can override this
@ -35,6 +39,8 @@ enum{NONE,LINEAR,SPLINE};
Bond::Bond(LAMMPS *lmp) : Pointers(lmp)
{
instance_me = instance_total++;
energy = 0.0;
virial[0] = virial[1] = virial[2] = virial[3] = virial[4] = virial[5] = 0.0;
writedata = 1;

3
src/bond.h
View File

@ -23,6 +23,8 @@ class Bond : protected Pointers {
friend class FixOMP;
public:
static int instance_total; // # of Bond classes ever instantiated
int allocated;
int *setflag;
int partial_flag; // 1 if bond type can be set to 0 and deleted
@ -68,6 +70,7 @@ class Bond : protected Pointers {
void write_file(int, char **);
protected:
int instance_me; // which Bond class instantiation I am
int suffix_flag; // suffix compatibility flag
int evflag;

2
src/fix_bond_history.cpp
View File

@ -308,4 +308,4 @@ void FixBondHistory::shift_bond(int i, int m, int k)
int n = atom->num_bond[i];
for (int idata = 0; idata < ndata; idata ++)
stored[i][m*ndata+idata] = stored[i][k*ndata+idata];
}
}

2
src/fix_bond_history.h
View File

@ -42,7 +42,7 @@ class FixBondHistory : public Fix {
void update_atom_value(int, int, int, double);
double get_atom_value(int, int, int);
void delete_bond(int,int);
void shift_bond(int,int,int);
void shift_bond(int,int,int);
double **bondstore;
int stored_flag;

59
src/fix_property_atom.cpp
View File

@ -38,6 +38,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
restart_peratom = 1;
wd_section = 1;
create_attribute = 1;
int iarg = 3;
nvalue = narg-iarg;
@ -554,24 +555,44 @@ void FixPropertyAtom::copy_arrays(int i, int j, int /*delflag*/)
atom->q[j] = atom->q[i];
else if (styles[nv] == RMASS)
atom->rmass[j] = atom->rmass[i];
else if (styles[nv] == IVEC) {
else if (styles[nv] == IVEC)
atom->ivector[index[nv]][j] = atom->ivector[index[nv]][i];
atom->ivector[index[nv]][i] = 0;
} else if (styles[nv] == DVEC) {
else if (styles[nv] == DVEC)
atom->dvector[index[nv]][j] = atom->dvector[index[nv]][i];
atom->dvector[index[nv]][i] = 0.0;
} else if (styles[nv] == IARRAY) {
else if (styles[nv] == IARRAY) {
ncol = cols[nv];
for (k = 0; k < ncol; k++) {
for (k = 0; k < ncol; k++)
atom->iarray[index[nv]][j][k] = atom->iarray[index[nv]][i][k];
atom->iarray[index[nv]][i][k] = 0;
}
} else if (styles[nv] == DARRAY) {
ncol = cols[nv];
for (k = 0; k < ncol; k++) {
for (k = 0; k < ncol; k++)
atom->darray[index[nv]][j][k] = atom->darray[index[nv]][i][k];
}
}
}
/* ----------------------------------------------------------------------
initialize one atom's storage values, called when atom is created
------------------------------------------------------------------------- */
void FixPropertyAtom::set_arrays(int i)
{
int k,ncol;
for (int nv = 0; nv < nvalue; nv++) {
if (styles[nv] == IVEC)
atom->ivector[index[nv]][i] = 0;
else if (styles[nv] == DVEC)
atom->dvector[index[nv]][i] = 0.0;
else if (styles[nv] == IARRAY) {
ncol = cols[nv];
for (k = 0; k < ncol; k++)
atom->iarray[index[nv]][i][k] = 0;
} else if (styles[nv] == DARRAY) {
ncol = cols[nv];
for (k = 0; k < ncol; k++)
atom->darray[index[nv]][i][k] = 0.0;
}
}
}
}
@ -706,24 +727,16 @@ int FixPropertyAtom::pack_exchange(int i, double *buf)
if (styles[nv] == MOLECULE) buf[m++] = ubuf(atom->molecule[i]).d;
else if (styles[nv] == CHARGE) buf[m++] = atom->q[i];
else if (styles[nv] == RMASS) buf[m++] = atom->rmass[i];
else if (styles[nv] == IVEC) {
buf[m++] = ubuf(atom->ivector[index[nv]][i]).d;
atom->ivector[index[nv]][i] = 0;
} else if (styles[nv] == DVEC) {
buf[m++] = atom->dvector[index[nv]][i];
atom->dvector[index[nv]][i] = 0.0;
} else if (styles[nv] == IARRAY) {
else if (styles[nv] == IVEC) buf[m++] = ubuf(atom->ivector[index[nv]][i]).d;
else if (styles[nv] == DVEC) buf[m++] = atom->dvector[index[nv]][i];
else if (styles[nv] == IARRAY) {
ncol = cols[nv];
for (k = 0; k < ncol; k++) {
for (k = 0; k < ncol; k++)
buf[m++] = ubuf(atom->iarray[index[nv]][i][k]).d;
atom->iarray[index[nv]][i][k] = 0;
}
} else if (styles[nv] == DARRAY) {
ncol = cols[nv];
for (k = 0; k < ncol; k++) {
for (k = 0; k < ncol; k++)
buf[m++] = atom->darray[index[nv]][i][k];
atom->darray[index[nv]][i][k] = 0.0;
}
}
}

1
src/fix_property_atom.h
View File

@ -40,6 +40,7 @@ class FixPropertyAtom : public Fix {
virtual void grow_arrays(int);
void copy_arrays(int, int, int);
void set_arrays(int);
int pack_border(int, int *, double *);
int unpack_border(int, int, double *);
int pack_exchange(int, double *);

2
src/fix_store_local.h
View File

@ -13,7 +13,7 @@
#ifdef FIX_CLASS
// clang-format off
FixStyle(store/local,FixStoreLocal);
FixStyle(STORE_LOCAL,FixStoreLocal);
// clang-format on
#else

130
src/BPM/fix_update_special_bonds.cpp → src/fix_update_special_bonds.cpp
View File

@ -24,7 +24,7 @@
#include "pair.h"
#include <cstring>
#include <set>
#include <vector>
#include <utility>
using namespace LAMMPS_NS;
@ -36,7 +36,6 @@ FixUpdateSpecialBonds::FixUpdateSpecialBonds(LAMMPS *lmp, int narg, char **arg)
Fix(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal fix update/special/bonds command");
comm_forward = 1+atom->maxspecial;
}
/* ---------------------------------------------------------------------- */
@ -76,6 +75,7 @@ void FixUpdateSpecialBonds::setup(int /*vflag*/)
force->special_coul[3] != 1.0)
error->all(FLERR,"Fix update/special/bonds requires special Coulomb weights = 1,1,1");
new_broken_pairs.clear();
broken_pairs.clear();
}
@ -86,7 +86,7 @@ void FixUpdateSpecialBonds::setup(int /*vflag*/)
void FixUpdateSpecialBonds::pre_exchange()
{
int i, j, key, m, n1, n3;
tagint min_tag, max_tag;
tagint tagi, tagj;
int nlocal = atom->nlocal;
tagint *tag = atom->tag;
@ -94,19 +94,19 @@ void FixUpdateSpecialBonds::pre_exchange()
int **nspecial = atom->nspecial;
tagint **special = atom->special;
for (auto const &key : broken_pairs) {
min_tag = key.first;
max_tag = key.second;
for (auto const &it : broken_pairs) {
tagi = it.first;
tagj = it.second;
i = atom->map(min_tag);
j = atom->map(max_tag);
i = atom->map(tagi);
j = atom->map(tagj);
// remove i from special bond list for atom j and vice versa
if (i < nlocal) {
slist = special[i];
n1 = nspecial[i][0];
for (m = 0; m < n1; m++)
if (slist[m] == max_tag) break;
if (slist[m] == tagj) break;
n3 = nspecial[i][2];
for (; m < n3-1; m++) slist[m] = slist[m+1];
nspecial[i][0]--;
@ -118,7 +118,7 @@ void FixUpdateSpecialBonds::pre_exchange()
slist = special[j];
n1 = nspecial[j][0];
for (m = 0; m < n1; m++)
if (slist[m] == min_tag) break;
if (slist[m] == tagi) break;
n3 = nspecial[j][2];
for (; m < n3-1; m++) slist[m] = slist[m+1];
nspecial[j][0]--;
@ -127,9 +127,6 @@ void FixUpdateSpecialBonds::pre_exchange()
}
}
// Forward updated special bond list
comm->forward_comm_fix(this);
broken_pairs.clear();
}
@ -139,82 +136,51 @@ void FixUpdateSpecialBonds::pre_exchange()
void FixUpdateSpecialBonds::pre_force(int /*vflag*/)
{
int i,j,n,m,ii,jj,inum,jnum;
int *ilist,*jlist,*numneigh,**firstneigh;
tagint min_tag, max_tag;
std::pair <tagint, tagint> key;
int i1,i2,j,jj,jnum;
int *jlist,*numneigh,**firstneigh;
tagint tag1, tag2;
int **bond_type = atom->bond_type;
int *num_bond = atom->num_bond;
tagint **bond_atom = atom->bond_atom;
int nlocal = atom->nlocal;
tagint *tag = atom->tag;
NeighList *list = force->pair->list;
inum = list->inum;
ilist = list->ilist;
NeighList *list = force->pair->list; // may need to be generalized to work with pair hybrid*
numneigh = list->numneigh;
firstneigh = list->firstneigh;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
jlist = firstneigh[i];
jnum = numneigh[i];
// In theory could communicate a list of broken bonds to neighboring processors here
// to remove restriction that users use Newton bond off
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
min_tag = tag[i];
max_tag = tag[j];
if (max_tag < min_tag) {
min_tag = tag[j];
max_tag = tag[i];
for (auto const &it : new_broken_pairs) {
tag1 = it.first;
tag2 = it.second;
i1 = atom->map(tag1);
i2 = atom->map(tag2);
// Loop through atoms of owned atoms i j
if (i1 < nlocal) {
jlist = firstneigh[i1];
jnum = numneigh[i1];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= SPECIALMASK; // Clear special bond bits
if (tag[j] == tag2)
jlist[jj] = j;
}
key = std::make_pair(min_tag, max_tag);
}
if (broken_pairs.find(key) != broken_pairs.end())
jlist[jj] = j; // Clear special bond bits
if (i2 < nlocal) {
jlist = firstneigh[i2];
jnum = numneigh[i2];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= SPECIALMASK; // Clear special bond bits
if (tag[j] == tag1)
jlist[jj] = j;
}
}
}
}
/* ---------------------------------------------------------------------- */
int FixUpdateSpecialBonds::pack_forward_comm(int n, int *list, double *buf,
int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,k,m,ns;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
ns = nspecial[j][0];
buf[m++] = ubuf(ns).d;
for (k = 0; k < ns; k++)
buf[m++] = ubuf(special[j][k]).d;
}
return m;
}
/* ---------------------------------------------------------------------- */
void FixUpdateSpecialBonds::unpack_forward_comm(int n, int first, double *buf)
{
int i,j,m,ns,last;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
ns = (int) ubuf(buf[m++]).i;
nspecial[i][0] = ns;
for (j = 0; j < ns; j++)
special[i][j] = (tagint) ubuf(buf[m++]).i;
}
new_broken_pairs.clear();
}
/* ---------------------------------------------------------------------- */
@ -222,14 +188,8 @@ void FixUpdateSpecialBonds::unpack_forward_comm(int n, int first, double *buf)
void FixUpdateSpecialBonds::add_broken_bond(int i, int j)
{
tagint *tag = atom->tag;
std::pair <tagint, tagint> tag_pair = std::make_pair(tag[i],tag[j]);
tagint min_tag = tag[i];
tagint max_tag = tag[j];
if (max_tag < min_tag) {
min_tag = tag[j];
max_tag = tag[i];
}
std::pair <tagint, tagint> key = std::make_pair(min_tag, max_tag);
broken_pairs.insert(key);
new_broken_pairs.push_back(tag_pair);
broken_pairs.push_back(tag_pair);
}

14
src/BPM/fix_update_special_bonds.h → src/fix_update_special_bonds.h
View File

@ -22,7 +22,7 @@ FixStyle(UPDATE_SPECIAL_BONDS,FixUpdateSpecialBonds)
#include "fix.h"
#include <set>
#include <vector>
#include <utility>
namespace LAMMPS_NS {
@ -34,16 +34,14 @@ class FixUpdateSpecialBonds : public Fix {
int setmask();
void setup(int);
void pre_exchange();
void pre_force(int);
int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *);
void pre_force(int);
void add_broken_bond(int,int);
protected:
std::set <std::pair<tagint, tagint>> broken_pairs;
inline int sbmask(int j) const {
return j >> SBBITS & 3;
}
// Create two arrays to store bonds broken this timestep (new)
// and since the last neighbor list build
std::vector <std::pair<tagint, tagint>> new_broken_pairs;
std::vector <std::pair<tagint, tagint>> broken_pairs;
};
} // namespace LAMMPS_NS

5
src/lmptype.h
View File

@ -55,14 +55,15 @@
namespace LAMMPS_NS {
// reserve 2 hi bits in molecular system neigh list for special bonds flag
// reserve 3rd last bit in neigh list for fix neigh/history flag
// reserve 2 highest bits in molecular system neigh list for special bonds flag
// reserve 3rd highest bit in neigh list for fix neigh/history flag
// max local + ghost atoms per processor = 2^29 - 1
#define SBBITS 30
#define HISTBITS 29
#define NEIGHMASK 0x1FFFFFFF
#define HISTMASK 0xDFFFFFFF
#define SPECIALMASK 0x3FFFFFFF
// default to 32-bit smallint and other ints, 64-bit bigint