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corrections to documentation and implementation of pair styles lj/mdf, buck/mdf, and lennard/mdf

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This commit is contained in:
Axel Kohlmeyer
2019-05-07 19:52:00 -04:00
parent 45e6ed018e
commit 711cd4122f
4 changed files with 37 additions and 83 deletions
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68
doc/src/pair_mdf.txt
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@ -30,16 +30,16 @@ args = list of arguments for a particular style :l
[Examples:]
pair_style lj/mdf 2.5 3.0
pair_coeff * * 1 1
pair_coeff 1 1 1 1.1 2.8 3.0 3.2 :pre
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.1 2.8 3.0 3.2 :pre
pair_style buck 2.5 3.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff * * 100.0 1.5 200.0 3.0 3.5 :pre
pair_style lennard/mdf 2.5 3.0
pair_coeff * * 1 1
pair_coeff 1 1 1 1.1 2.8 3.0 3.2 :pre
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1021760.3664 2120.317338 3.0 3.2 :pre
[Description:]
@ -69,11 +69,12 @@ standard 12-6 Lennard-Jones written in the epsilon/sigma form:
:c,image(Eqs/pair_mdf-4.jpg)
The following coefficients must be defined for each pair of atoms
types via the pair_coeff command as in the examples above, or in the
data file or restart files read by the "read_data"_read_data.html or
"read_restart commands"_read_restart.html, or by mixing as described
below:
Either the first two or all of the following coefficients must be
defined for each pair of atoms types via the pair_coeff command as
in the examples above, or in the data file read by the
"read_data"_read_data.html. The two cutoffs default to the global
values and epsilon and sigma can also be determined by mixing as
described below:
epsilon (energy units)
sigma (distance units)
@ -83,7 +84,9 @@ r_{cut} (distance units) :ul
:line
For the {buck/mdf} pair_style, the potential energy, {E(r)}, is the
standard Buckingham potential:
standard Buckingham potential with three required coefficients.
The two cutoffs can be omitted and default to the corresponding
global values:
:c,image(Eqs/pair_mdf-5.jpg)
@ -91,19 +94,20 @@ A (energy units)
\rho (distance units)
C (energy-distance^6 units)
r_m (distance units)
r_{cut}$ (distance units) :ul
r_{cut} (distance units) :ul
:line
For the {lennard/mdf} pair_style, the potential energy, {E(r)}, is the
standard 12-6 Lennard-Jones written in the $A/B$ form:
standard 12-6 Lennard-Jones written in the A/B form:
:c,image(Eqs/pair_mdf-6.jpg)
The following coefficients must be defined for each pair of atoms
types via the pair_coeff command as in the examples above, or in the
data file or restart files read by the read_data or read_restart
commands, or by mixing as described below:
data file read by the read_data commands, or by mixing as described below.
The two cutoffs default to their global values and must be either both
given or both left out:
A (energy-distance^12 units)
B (energy-distance^6 units)
@ -115,33 +119,23 @@ r_{cut} (distance units) :ul
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
and cutoff distances for the lj/mdf pair style can be mixed.
The default mix value is {geometric}. See the "pair_modify" command
for details.
for details. The other two pair styles buck/mdf and lennard/mdf do not
support mixing, so all I,J pairs of coefficients must be specified
explicitly.
All of the {lj/cut} pair styles support the
"pair_modify"_pair_modify.html shift option for the energy of the
Lennard-Jones portion of the pair interaction.
None of the lj/mdf, buck/mdf, or lennard/mdf pair styles supports
the "pair_modify"_pair_modify.html shift option or long-range
tail corrections to pressure and energy.
The {lj/cut/coul/long} and {lj/cut/tip4p/long} pair styles support the
"pair_modify"_pair_modify.html table option since they can tabulate
the short-range portion of the long-range Coulombic interaction.
These styles write their information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
All of the {lj/cut} pair styles support the
"pair_modify"_pair_modify.html tail option for adding a long-range
tail correction to the energy and pressure for the Lennard-Jones
portion of the pair interaction.
All of the {lj/cut} pair styles write their information to "binary
restart files"_restart.html, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
The {lj/cut} and {lj/cut/coul/long} pair styles support the use of the
{inner}, {middle}, and {outer} keywords of the "run_style
respa"_run_style.html command, meaning the pairwise forces can be
partitioned by distance at different levels of the rRESPA hierarchy.
The other styles only support the {pair} keyword of run_style respa.
See the "run_style"_run_style.html command for details.
These styles can only be used via the {pair} keyword of the "run_style
respa"_run_style.html command. They do not support the {inner},
{middle}, {outer} keywords.
:line

40
src/USER-MISC/pair_buck_mdf.cpp
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@ -52,7 +52,6 @@ PairBuckMDF::~PairBuckMDF()
memory->destroy(rhoinv);
memory->destroy(buck1);
memory->destroy(buck2);
memory->destroy(offset);
}
}
@ -177,7 +176,6 @@ void PairBuckMDF::allocate()
memory->create(rhoinv,n+1,n+1,"pair:rhoinv");
memory->create(buck1,n+1,n+1,"pair:buck1");
memory->create(buck2,n+1,n+1,"pair:buck2");
memory->create(offset,n+1,n+1,"pair:offset");
}
/* ----------------------------------------------------------------------
@ -207,7 +205,8 @@ void PairBuckMDF::settings(int narg, char **arg)
void PairBuckMDF::coeff(int narg, char **arg)
{
if (narg != 5 && narg != 7) error->all(FLERR,"Incorrect args for pair coefficients");
if (narg != 5 && narg != 7)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
@ -258,11 +257,6 @@ double PairBuckMDF::init_one(int i, int j)
buck1[i][j] = a[i][j]/rho[i][j];
buck2[i][j] = 6.0*c[i][j];
if (offset_flag && (cut[i][j] > 0.0)) {
double rexp = exp(-cut[i][j]/rho[i][j]);
offset[i][j] = a[i][j]*rexp - c[i][j]/pow(cut[i][j],6.0);
} else offset[i][j] = 0.0;
cut_inner[j][i] = cut_inner[i][j];
cut_inner_sq[i][j] = cut_inner[i][j]*cut_inner[i][j];
cut_inner_sq[j][i] = cut_inner_sq[i][j];
@ -272,36 +266,6 @@ double PairBuckMDF::init_one(int i, int j)
rhoinv[j][i] = rhoinv[i][j];
buck1[j][i] = buck1[i][j];
buck2[j][i] = buck2[i][j];
offset[j][i] = offset[i][j];
// compute I,J contribution to long-range tail correction
// count total # of atoms of type I and J via Allreduce
if (tail_flag) {
int *type = atom->type;
int nlocal = atom->nlocal;
double count[2],all[2];
count[0] = count[1] = 0.0;
for (int k = 0; k < nlocal; k++) {
if (type[k] == i) count[0] += 1.0;
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
double rho1 = rho[i][j];
double rho2 = rho1*rho1;
double rho3 = rho2*rho1;
double rc = cut[i][j];
double rc2 = rc*rc;
double rc3 = rc2*rc;
etail_ij = 2.0*MY_PI*all[0]*all[1]*
(a[i][j]*exp(-rc/rho1)*rho1*(rc2 + 2.0*rho1*rc + 2.0*rho2) -
c[i][j]/(3.0*rc3));
ptail_ij = (-1/3.0)*2.0*MY_PI*all[0]*all[1]*
(-a[i][j]*exp(-rc/rho1)*
(rc3 + 3.0*rho1*rc2 + 6.0*rho2*rc + 6.0*rho3) + 2.0*c[i][j]/rc3);
}
return cut[i][j];
}

8
src/USER-MISC/pair_lennard_mdf.cpp
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@ -251,13 +251,7 @@ void PairLJ_AB_MDF::coeff(int narg, char **arg)
double PairLJ_AB_MDF::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
aparm[i][j] = mix_energy(aparm[i][i],aparm[j][j],
bparm[i][i],bparm[j][j]);
bparm[i][j] = mix_distance(bparm[i][i],bparm[j][j]);
cut_inner[i][j] = mix_distance(cut_inner[i][i],cut_inner[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
cut_inner_sq[i][j] = cut_inner[i][j]*cut_inner[i][j];

4
src/USER-MISC/pair_lj_mdf.cpp
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@ -33,7 +33,9 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairLJMDF::PairLJMDF(LAMMPS *lmp) : Pair(lmp) {}
PairLJMDF::PairLJMDF(LAMMPS *lmp) : Pair(lmp) {
writedata = 1;
}
/* ---------------------------------------------------------------------- */