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support providing spring constant as equal or atom style variable

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This commit is contained in:
Axel Kohlmeyer
2024-11-15 14:12:19 -05:00
parent ae1c5651ef
commit 4dd1448dd0
5 changed files with 256 additions and 22 deletions
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19
doc/src/fix_spring_self.rst
View File

@ -13,7 +13,7 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command
* spring/self = style name of this fix command
* K = spring constant (force/distance units)
* K = spring constant (force/distance units), can be a variable (see below)
* dir = xyz, xy, xz, yz, x, y, or z (optional, default: xyz)
Examples
@ -22,6 +22,7 @@ Examples
.. code-block:: LAMMPS
fix tether boundary-atoms spring/self 10.0
fix var all spring/self v_kvar
fix zrest move spring/self 10.0 z
Description
@ -42,6 +43,22 @@ directions, but it can be limited to the xy-, xz-, yz-plane and the
x-, y-, or z-direction, thus restraining the atoms to a line or a
plane, respectively.
The force constant *k* can be specified as an equal-style or atom-style
:doc:`variable <variable>`. If the value is a variable, it should be specified
as v_name, where name is the variable name. In this case, the variable
will be evaluated each time step, and its value(s) will be used as
force constant for the spring force.
Equal-style variables can specify formulas with various mathematical
functions and include :doc:`thermo_style <thermo_style>` command
keywords for the simulation box parameters, time step, and elapsed time.
Thus, it is easy to specify a time-dependent force field.
Atom-style variables can specify the same formulas as equal-style
variables but can also include per-atom values, such as atom
coordinates. Thus, it is easy to specify a spatially-dependent force
field with optional time-dependence as well.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

100
src/fix_spring_self.cpp
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@ -21,20 +21,23 @@
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "input.h"
#include "memory.h"
#include "respa.h"
#include "update.h"
#include "variable.h"
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;
enum { NONE, CONSTANT, EQUAL, ATOM };
/* ---------------------------------------------------------------------- */
FixSpringSelf::FixSpringSelf(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
xoriginal(nullptr)
Fix(lmp, narg, arg), xoriginal(nullptr), kstr(nullptr)
{
if ((narg < 4) || (narg > 5))
error->all(FLERR,"Illegal fix spring/self command");
@ -46,8 +49,14 @@ FixSpringSelf::FixSpringSelf(LAMMPS *lmp, int narg, char **arg) :
energy_global_flag = 1;
respa_level_support = 1;
k = utils::numeric(FLERR,arg[3],false,lmp);
if (k <= 0.0) error->all(FLERR,"Illegal fix spring/self command");
if (utils::strmatch(arg[3], "^v_")) {
kstr = utils::strdup(arg[3] + 2);
kstyle = NONE;
} else {
k = utils::numeric(FLERR,arg[3],false,lmp);
kstyle = CONSTANT;
if (k <= 0.0) error->all(FLERR,"Illegal force constatnt for fix spring/self command");
}
xflag = yflag = zflag = 1;
@ -123,6 +132,25 @@ int FixSpringSelf::setmask()
void FixSpringSelf::init()
{
// check variable
if (kstr) {
kvar = input->variable->find(kstr);
if (kvar < 0) error->all(FLERR, "Variable {} for fix spring/self does not exist", kstr);
if (input->variable->equalstyle(kvar))
kstyle = EQUAL;
else if (input->variable->atomstyle(kvar))
kstyle = ATOM;
else
error->all(FLERR, "Variable {} for fix spring/self is invalid style", kstr);
}
if ((kstyle == ATOM) && (atom->nmax > maxatom)) {
maxatom = atom->nmax;
memory->destroy(kval);
memory->create(kval, maxatom, "sprint/self:kval");
}
if (utils::strmatch(update->integrate_style,"^respa")) {
ilevel_respa = (dynamic_cast<Respa *>(update->integrate))->nlevels-1;
if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa);
@ -162,24 +190,55 @@ void FixSpringSelf::post_force(int /*vflag*/)
double dx,dy,dz;
double unwrap[3];
// reallocate kval array if necessary
if ((kstyle == ATOM) && (atom->nmax > maxatom)) {
maxatom = atom->nmax;
memory->destroy(kval);
memory->create(kval, maxatom, "sprint/self:kval");
}
espring = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - xoriginal[i][0];
dy = unwrap[1] - xoriginal[i][1];
dz = unwrap[2] - xoriginal[i][2];
if (!xflag) dx = 0.0;
if (!yflag) dy = 0.0;
if (!zflag) dz = 0.0;
f[i][0] -= k*dx;
f[i][1] -= k*dy;
f[i][2] -= k*dz;
espring += k * (dx*dx + dy*dy + dz*dz);
}
if ((kstyle == CONSTANT) || (kstyle == EQUAL)) {
// update k if equal style variable
if (kstyle == EQUAL) k = input->variable->compute_equal(kvar);
espring *= 0.5;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - xoriginal[i][0];
dy = unwrap[1] - xoriginal[i][1];
dz = unwrap[2] - xoriginal[i][2];
if (!xflag) dx = 0.0;
if (!yflag) dy = 0.0;
if (!zflag) dz = 0.0;
f[i][0] -= k*dx;
f[i][1] -= k*dy;
f[i][2] -= k*dz;
espring += k * (dx*dx + dy*dy + dz*dz);
}
espring *= 0.5;
} else {
// update kval for kstyle == ATOM
input->variable->compute_atom(kvar, igroup, kval, 1, 0);
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - xoriginal[i][0];
dy = unwrap[1] - xoriginal[i][1];
dz = unwrap[2] - xoriginal[i][2];
if (!xflag) dx = 0.0;
if (!yflag) dy = 0.0;
if (!zflag) dz = 0.0;
f[i][0] -= kval[i]*dx;
f[i][1] -= kval[i]*dy;
f[i][2] -= kval[i]*dz;
espring += kval[i] * (dx*dx + dy*dy + dz*dz);
}
espring *= 0.5;
}
}
/* ---------------------------------------------------------------------- */
@ -213,7 +272,8 @@ double FixSpringSelf::compute_scalar()
double FixSpringSelf::memory_usage()
{
double bytes = (double)atom->nmax*3 * sizeof(double);
double bytes = (double)atom->nmax*4 * sizeof(double);
if (kstyle == ATOM) bytes += (double)atom->nmax * sizeof(double);
return bytes;
}

5
src/fix_spring_self.h
View File

@ -50,8 +50,11 @@ class FixSpringSelf : public Fix {
protected:
double k, espring;
double **xoriginal; // original coords of atoms
char *kstr; // name of variable for K
double *kval; // per-atom variable values for K
int kvar, kstyle;
int xflag, yflag, zflag;
int ilevel_respa;
int ilevel_respa, maxatom;
};
} // namespace LAMMPS_NS

77
unittest/force-styles/tests/fix-timestep-spring_self_atom.yaml Normal file
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@ -0,0 +1,77 @@
---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:01 2022
epsilon: 5e-14
skip_tests: kokkos_omp
prerequisites: ! |
atom full
fix spring/self
pre_commands: ! |
variable kvar atom 10.0
post_commands: ! |
fix move all nve
fix test solute spring/self v_kvar xyz
input_file: in.fourmol
natoms: 29
global_scalar: 0.12623705370750438
run_pos: ! |2
1 -2.7045669792379945e-01 2.4912140072031601e+00 -1.6695897908630153e-01
2 3.1003572362014503e-01 2.9612290242130319e+00 -8.5466689099875615e-01
3 -7.0398410505917419e-01 1.2305522448803927e+00 -6.2777452858703953e-01
4 -1.5818137373512378e+00 1.4837442978868092e+00 -1.2538665277734968e+00
5 -9.0719266809604937e-01 9.2652365891304722e-01 3.9954299416556610e-01
6 2.4832271436421161e-01 2.8312320769893828e-01 -1.2314303818391423e+00
7 3.4143518373063453e-01 -2.2645187306940717e-02 -2.5292229406165907e+00
8 1.1743540824610306e+00 -4.8863162985819381e-01 -6.3783828665914544e-01
9 1.3800508883119953e+00 -2.5274565574966718e-01 2.8353436538531862e-01
10 2.0510726036138696e+00 -1.4604027090169940e+00 -9.8323554549077119e-01
11 1.7878052123899795e+00 -1.9921835931655048e+00 -1.8890566136917575e+00
12 3.0063000763288268e+00 -4.9013323763786637e-01 -1.6231890083142151e+00
13 4.0515352007695906e+00 -8.9202569828585798e-01 -1.6399995011867139e+00
14 2.6066952690925067e+00 -4.1788633645045253e-01 -2.6633949696742012e+00
15 2.9695337662435719e+00 5.5423141568538492e-01 -1.2342076641871542e+00
16 2.6747001492056977e+00 -2.4124097322472577e+00 -2.3429048072365732e-02
17 2.2153591049025310e+00 -2.0897997214660862e+00 1.1963106355359285e+00
18 2.1369701704115056e+00 3.0158507413628213e+00 -3.5179348337213843e+00
19 1.5355837136087338e+00 2.6255292355375399e+00 -4.2353987779878857e+00
20 2.7727573005678758e+00 3.6923910449610102e+00 -3.9330842459133470e+00
21 4.9040128073205524e+00 -4.0752348172959030e+00 -3.6210314709893159e+00
22 4.3582355554440877e+00 -4.2126119427287101e+00 -4.4612844196314150e+00
23 5.7439382849307670e+00 -3.5821957939275060e+00 -3.8766361295935892e+00
24 2.0689243582422914e+00 3.1513346907271247e+00 3.1550389754829422e+00
25 1.3045351331492516e+00 3.2665125705842941e+00 2.5111855257434352e+00
26 2.5809237402711318e+00 4.0117602605482858e+00 3.2212060529089945e+00
27 -1.9611343130357277e+00 -4.3563411931359841e+00 2.1098293115523528e+00
28 -2.7473562684513411e+00 -4.0200819932379330e+00 1.5830052163433952e+00
29 -1.3126000191359812e+00 -3.5962518039482934e+00 2.2746342468737817e+00
run_vel: ! |2
1 8.1685220941861477e-03 1.6512578512542727e-02 4.7892799147935001e-03
2 5.4427456394786321e-03 5.1693257879352533e-03 -1.4414043022813649e-03
3 -8.2272458036248362e-03 -1.2923813188884230e-02 -4.0970749471144546e-03
4 -3.7660861920462349e-03 -6.5659911420830365e-03 -1.1120922532834726e-03
5 -1.1012635909013241e-02 -9.8847866026321157e-03 -2.8391869073674538e-03
6 -3.9665990411620729e-02 4.6803722380071487e-02 3.7135522426802389e-02
7 9.1016763589152859e-04 -1.0126055720737583e-02 -5.1556610019025714e-02
8 7.9043585267658430e-03 -3.3496064544244345e-03 3.4549326598010660e-02
9 1.5620907286754389e-03 3.7378245105921431e-03 1.5036774253075934e-02
10 2.9193799040059056e-02 -2.9242248165535563e-02 -1.5014281912567770e-02
11 -4.7797459644718264e-03 -3.7436196398511232e-03 -2.3410499103477603e-03
12 2.2686069875175316e-03 -3.4732729502899497e-04 -3.0627334265471650e-03
13 2.7456854188010020e-03 5.8081889921879817e-03 -7.9308949311655092e-04
14 3.5223319737918667e-03 -5.7842699330258648e-03 -3.9396805101296825e-03
15 -1.8475459117759364e-03 -5.8469790281561471e-03 6.2849983323582511e-03
16 1.8676069228413028e-02 -1.3258381729410438e-02 -4.5625616778429308e-02
17 -1.2893668780819389e-02 9.7505325833410258e-03 3.7288200735675299e-02
18 -8.0065794869105819e-04 -8.6270473288011819e-04 -1.4483040693746142e-03
19 1.2452390836051499e-03 -2.5061097119616180e-03 7.2998631010316650e-03
20 3.5930060229538143e-03 3.6938860309035470e-03 3.2322732687958995e-03
21 -1.4689220366910704e-03 -2.7352129796142532e-04 7.0581624168175334e-04
22 -7.0694199254520765e-03 -4.2577148925037030e-03 2.8079117611209205e-04
23 6.0446963117617505e-03 -1.4000131614895336e-03 2.5819754846773601e-03
24 3.1926367911308686e-04 -9.9445664741642462e-04 1.4999996978363057e-04
25 1.3789754526895179e-04 -4.4335894884219599e-03 -8.1808136698604454e-04
26 2.0485904035342870e-03 2.7813358633902757e-03 4.3245727149365584e-03
27 4.5604120291626942e-04 -1.0305523027244966e-03 2.1188058375789067e-04
28 -6.2544520861839200e-03 1.4127711176141612e-03 -1.8429821884806304e-03
29 6.4110631535703737e-04 3.1273432719578029e-03 3.7253671105604122e-03
...

77
unittest/force-styles/tests/fix-timestep-spring_self_equal.yaml Normal file
View File

@ -0,0 +1,77 @@
---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:01 2022
epsilon: 5e-14
skip_tests: kokkos_omp
prerequisites: ! |
atom full
fix spring/self
pre_commands: ! |
variable kvar equal 10.0
post_commands: ! |
fix move all nve
fix test solute spring/self v_kvar xyz
input_file: in.fourmol
natoms: 29
global_scalar: 0.12623705370750438
run_pos: ! |2
1 -2.7045669792379945e-01 2.4912140072031601e+00 -1.6695897908630153e-01
2 3.1003572362014503e-01 2.9612290242130319e+00 -8.5466689099875615e-01
3 -7.0398410505917419e-01 1.2305522448803927e+00 -6.2777452858703953e-01
4 -1.5818137373512378e+00 1.4837442978868092e+00 -1.2538665277734968e+00
5 -9.0719266809604937e-01 9.2652365891304722e-01 3.9954299416556610e-01
6 2.4832271436421161e-01 2.8312320769893828e-01 -1.2314303818391423e+00
7 3.4143518373063453e-01 -2.2645187306940717e-02 -2.5292229406165907e+00
8 1.1743540824610306e+00 -4.8863162985819381e-01 -6.3783828665914544e-01
9 1.3800508883119953e+00 -2.5274565574966718e-01 2.8353436538531862e-01
10 2.0510726036138696e+00 -1.4604027090169940e+00 -9.8323554549077119e-01
11 1.7878052123899795e+00 -1.9921835931655048e+00 -1.8890566136917575e+00
12 3.0063000763288268e+00 -4.9013323763786637e-01 -1.6231890083142151e+00
13 4.0515352007695906e+00 -8.9202569828585798e-01 -1.6399995011867139e+00
14 2.6066952690925067e+00 -4.1788633645045253e-01 -2.6633949696742012e+00
15 2.9695337662435719e+00 5.5423141568538492e-01 -1.2342076641871542e+00
16 2.6747001492056977e+00 -2.4124097322472577e+00 -2.3429048072365732e-02
17 2.2153591049025310e+00 -2.0897997214660862e+00 1.1963106355359285e+00
18 2.1369701704115056e+00 3.0158507413628213e+00 -3.5179348337213843e+00
19 1.5355837136087338e+00 2.6255292355375399e+00 -4.2353987779878857e+00
20 2.7727573005678758e+00 3.6923910449610102e+00 -3.9330842459133470e+00
21 4.9040128073205524e+00 -4.0752348172959030e+00 -3.6210314709893159e+00
22 4.3582355554440877e+00 -4.2126119427287101e+00 -4.4612844196314150e+00
23 5.7439382849307670e+00 -3.5821957939275060e+00 -3.8766361295935892e+00
24 2.0689243582422914e+00 3.1513346907271247e+00 3.1550389754829422e+00
25 1.3045351331492516e+00 3.2665125705842941e+00 2.5111855257434352e+00
26 2.5809237402711318e+00 4.0117602605482858e+00 3.2212060529089945e+00
27 -1.9611343130357277e+00 -4.3563411931359841e+00 2.1098293115523528e+00
28 -2.7473562684513411e+00 -4.0200819932379330e+00 1.5830052163433952e+00
29 -1.3126000191359812e+00 -3.5962518039482934e+00 2.2746342468737817e+00
run_vel: ! |2
1 8.1685220941861477e-03 1.6512578512542727e-02 4.7892799147935001e-03
2 5.4427456394786321e-03 5.1693257879352533e-03 -1.4414043022813649e-03
3 -8.2272458036248362e-03 -1.2923813188884230e-02 -4.0970749471144546e-03
4 -3.7660861920462349e-03 -6.5659911420830365e-03 -1.1120922532834726e-03
5 -1.1012635909013241e-02 -9.8847866026321157e-03 -2.8391869073674538e-03
6 -3.9665990411620729e-02 4.6803722380071487e-02 3.7135522426802389e-02
7 9.1016763589152859e-04 -1.0126055720737583e-02 -5.1556610019025714e-02
8 7.9043585267658430e-03 -3.3496064544244345e-03 3.4549326598010660e-02
9 1.5620907286754389e-03 3.7378245105921431e-03 1.5036774253075934e-02
10 2.9193799040059056e-02 -2.9242248165535563e-02 -1.5014281912567770e-02
11 -4.7797459644718264e-03 -3.7436196398511232e-03 -2.3410499103477603e-03
12 2.2686069875175316e-03 -3.4732729502899497e-04 -3.0627334265471650e-03
13 2.7456854188010020e-03 5.8081889921879817e-03 -7.9308949311655092e-04
14 3.5223319737918667e-03 -5.7842699330258648e-03 -3.9396805101296825e-03
15 -1.8475459117759364e-03 -5.8469790281561471e-03 6.2849983323582511e-03
16 1.8676069228413028e-02 -1.3258381729410438e-02 -4.5625616778429308e-02
17 -1.2893668780819389e-02 9.7505325833410258e-03 3.7288200735675299e-02
18 -8.0065794869105819e-04 -8.6270473288011819e-04 -1.4483040693746142e-03
19 1.2452390836051499e-03 -2.5061097119616180e-03 7.2998631010316650e-03
20 3.5930060229538143e-03 3.6938860309035470e-03 3.2322732687958995e-03
21 -1.4689220366910704e-03 -2.7352129796142532e-04 7.0581624168175334e-04
22 -7.0694199254520765e-03 -4.2577148925037030e-03 2.8079117611209205e-04
23 6.0446963117617505e-03 -1.4000131614895336e-03 2.5819754846773601e-03
24 3.1926367911308686e-04 -9.9445664741642462e-04 1.4999996978363057e-04
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26 2.0485904035342870e-03 2.7813358633902757e-03 4.3245727149365584e-03
27 4.5604120291626942e-04 -1.0305523027244966e-03 2.1188058375789067e-04
28 -6.2544520861839200e-03 1.4127711176141612e-03 -1.8429821884806304e-03
29 6.4110631535703737e-04 3.1273432719578029e-03 3.7253671105604122e-03
...