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Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes

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This commit is contained in:
Axel Kohlmeyer
2022-01-14 20:25:05 -05:00
parent e271a54802 11cc8a6a59
commit aa71ea6c40
4 changed files with 66 additions and 63 deletions
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9
src/MANYBODY/pair_eam_cd.cpp
View File

@ -499,10 +499,13 @@ void PairEAMCD::read_h_coeff(char *filename)
// Seek to end of file, read last part into a buffer and
// then skip over lines in buffer until reaching the end.
platform::fseek(fptr, platform::END_OF_FILE);
platform::fseek(fptr, platform::ftell(fptr) - MAXLINE);
if ( (platform::fseek(fptr, platform::END_OF_FILE) < 0)
|| (platform::fseek(fptr, platform::ftell(fptr) - MAXLINE) < 0))
error->one(FLERR,"Failure to seek to end-of-file for reading h(x) coeffs: {}",
utils::getsyserror());
char *buf = new char[MAXLINE+1];
fread(buf, 1, MAXLINE, fptr);
utils::sfread(FLERR, buf, 1, MAXLINE, fptr, filename, error);
buf[MAXLINE] = '\0'; // must 0-terminate buffer for string processing
Tokenizer lines(buf, "\n");
delete[] buf;

6
src/REAXFF/fix_reaxff_species.cpp
View File

@ -246,8 +246,10 @@ FixReaxFFSpecies::~FixReaxFFSpecies()
if (posflag && multipos_opened) fclose(pos);
}
modify->delete_compute(fmt::format("SPECATOM_{}",id));
modify->delete_fix(fmt::format("SPECBOND_{}",id));
try {
modify->delete_compute(fmt::format("SPECATOM_{}",id));
modify->delete_fix(fmt::format("SPECBOND_{}",id));
} catch (std::exception &) {}
}
/* ---------------------------------------------------------------------- */

63
src/fix_move.cpp
View File

@ -522,7 +522,7 @@ void FixMove::initial_integrate(int /*vflag*/)
}
}
// for wiggle: X = X0 + A sin(w*dt)
// for wiggle: X = X0 + A sin(w*dt)
} else if (mstyle == WIGGLE) {
double arg = omega_rotate * delta;
@ -578,19 +578,19 @@ void FixMove::initial_integrate(int /*vflag*/)
}
}
// for rotate by right-hand rule around omega:
// P = point = vector = point of rotation
// R = vector = axis of rotation
// w = omega of rotation (from period)
// X0 = xoriginal = initial coord of atom
// R0 = runit = unit vector for R
// D = X0 - P = vector from P to X0
// C = (D dot R0) R0 = projection of atom coord onto R line
// A = D - C = vector from R line to X0
// B = R0 cross A = vector perp to A in plane of rotation
// A,B define plane of circular rotation around R line
// X = P + C + A cos(w*dt) + B sin(w*dt)
// V = w R0 cross (A cos(w*dt) + B sin(w*dt))
// for rotate by right-hand rule around omega:
// P = point = vector = point of rotation
// R = vector = axis of rotation
// w = omega of rotation (from period)
// X0 = xoriginal = initial coord of atom
// R0 = runit = unit vector for R
// D = X0 - P = vector from P to X0
// C = (D dot R0) R0 = projection of atom coord onto R line
// A = D - C = vector from R line to X0
// B = R0 cross A = vector perp to A in plane of rotation
// A,B define plane of circular rotation around R line
// X = P + C + A cos(w*dt) + B sin(w*dt)
// V = w R0 cross (A cos(w*dt) + B sin(w*dt))
} else if (mstyle == ROTATE) {
double arg = omega_rotate * delta;
@ -707,10 +707,10 @@ void FixMove::initial_integrate(int /*vflag*/)
}
}
// for variable: compute x,v from variables
// NOTE: also allow for changes to extra attributes?
// omega, angmom, theta, quat
// only necessary if prescribed motion involves rotation
// for variable: compute x,v from variables
// NOTE: also allow for changes to extra attributes?
// omega, angmom, theta, quat
// only necessary if prescribed motion involves rotation
} else if (mstyle == VARIABLE) {
@ -778,21 +778,16 @@ void FixMove::initial_integrate(int /*vflag*/)
} else if (vxvarstr) {
if (vxvarstyle == EQUAL) v[i][0] = vx;
else v[i][0] = velocity[i][0];
if (rmass) {
x[i][0] += dtv * v[i][0];
} else {
x[i][0] += dtv * v[i][0];
}
x[i][0] += dtv * v[i][0];
} else {
if (rmass) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
x[i][0] += dtv * v[i][0];
} else {
dtfm = dtf / mass[type[i]];
v[i][0] += dtfm * f[i][0];
x[i][0] += dtv * v[i][0];
}
x[i][0] += dtv * v[i][0];
}
if (yvarstr && vyvarstr) {
@ -806,21 +801,16 @@ void FixMove::initial_integrate(int /*vflag*/)
} else if (vyvarstr) {
if (vyvarstyle == EQUAL) v[i][1] = vy;
else v[i][1] = velocity[i][1];
if (rmass) {
x[i][1] += dtv * v[i][1];
} else {
x[i][1] += dtv * v[i][1];
}
x[i][1] += dtv * v[i][1];
} else {
if (rmass) {
dtfm = dtf / rmass[i];
v[i][1] += dtfm * f[i][1];
x[i][1] += dtv * v[i][1];
} else {
dtfm = dtf / mass[type[i]];
v[i][1] += dtfm * f[i][1];
x[i][1] += dtv * v[i][1];
}
x[i][1] += dtv * v[i][1];
}
if (zvarstr && vzvarstr) {
@ -834,21 +824,16 @@ void FixMove::initial_integrate(int /*vflag*/)
} else if (vzvarstr) {
if (vzvarstyle == EQUAL) v[i][2] = vz;
else v[i][2] = velocity[i][2];
if (rmass) {
x[i][2] += dtv * v[i][2];
} else {
x[i][2] += dtv * v[i][2];
}
x[i][2] += dtv * v[i][2];
} else {
if (rmass) {
dtfm = dtf / rmass[i];
v[i][2] += dtfm * f[i][2];
x[i][2] += dtv * v[i][2];
} else {
dtfm = dtf / mass[type[i]];
v[i][2] += dtfm * f[i][2];
x[i][2] += dtv * v[i][2];
}
x[i][2] += dtv * v[i][2];
}
domain->remap_near(x[i],xold);

51
src/output.cpp
View File

@ -41,6 +41,8 @@ using namespace LAMMPS_NS;
#define DELTA 1
#define EPSDT 1.0e-6
enum {SETUP, WRITE, RESET_DT};
/* ----------------------------------------------------------------------
initialize all output
------------------------------------------------------------------------- */
@ -232,7 +234,7 @@ void Output::setup(int memflag)
// only do this if dump written or dump has not been written yet
if (writeflag || last_dump[idump] < 0)
calculate_next_dump(0,idump,ntimestep);
calculate_next_dump(SETUP,idump,ntimestep);
// if dump not written now, use addstep_compute_all()
// since don't know what computes the dump will invoke
@ -361,7 +363,7 @@ void Output::setup(int memflag)
dump[idump]->write();
last_dump[idump] = ntimestep;
calculate_next_dump(1,idump,ntimestep);
calculate_next_dump(WRITE,idump,ntimestep);
if (mode_dump[idump] == 0 &&
(dump[idump]->clearstep || var_dump[idump]))
@ -468,12 +470,12 @@ void Output::setup(int memflag)
for timestep mode, set next_dump
for simulation time mode, set next_time_dump and next_dump
which flag depends on caller
0 = from setup() at start of run
1 = from write() during run each time a dump file is written
2 = from reset_dt() called from fix dt/reset when it changes timestep size
SETUP = from setup() at start of run
WRITE = from write() during run each time a dump file is written
RESET_DT = from reset_dt() called from fix dt/reset when it changes timestep size
------------------------------------------------------------------------- */
void Output::calculate_next_dump(int which, int idump, bigint ntimestep)
void Output::calculate_next_dump(int which, int idump, bigint ntimestep)
{
// dump mode is by timestep
// just set next_dump
@ -482,13 +484,13 @@ void Output::setup(int memflag)
if (every_dump[idump]) {
// which = 0: nextdump = next multiple of every_dump
// which = 1: increment nextdump by every_dump
// which = SETUP: nextdump = next multiple of every_dump
// which = WRITE: increment nextdump by every_dump
if (which == 0)
if (which == SETUP)
next_dump[idump] =
(ntimestep/every_dump[idump])*every_dump[idump] + every_dump[idump];
else if (which == 1)
else if (which == WRITE)
next_dump[idump] += every_dump[idump];
} else {
@ -510,17 +512,28 @@ void Output::setup(int memflag)
if (every_time_dump[idump] > 0.0) {
// which = 0: nexttime = next multiple of every_time_dump
// which = 1: increment nexttime by every_time_dump
// which = 2: no change to previous nexttime (only timestep has changed)
// which = SETUP: nexttime = next multiple of every_time_dump
// which = WRITE: increment nexttime by every_time_dump
// which = RESET_DT: no change to previous nexttime (only timestep has changed)
if (which == 0)
switch (which) {
case SETUP:
nexttime = static_cast<bigint> (tcurrent/every_time_dump[idump]) *
every_time_dump[idump] + every_time_dump[idump];
else if (which == 1)
break;
case WRITE:
nexttime = next_time_dump[idump] + every_time_dump[idump];
else if (which == 2)
break;
case RESET_DT:
nexttime = next_time_dump[idump];
break;
default:
nexttime = 0;
error->all(FLERR,"Unexpected argument to calculate_next_dump");
}
nextdump = ntimestep +
static_cast<bigint> ((nexttime - tcurrent - EPSDT*update->dt) /
@ -541,10 +554,10 @@ void Output::setup(int memflag)
} else {
// do not re-evaulate variable for which = 2, leave nexttime as-is
// do not re-evaulate variable for which = RESET_DT, leave nexttime as-is
// unless next_time_dump < 0.0, which means variable never yet evaluated
if (which < 2 || next_time_dump[idump] < 0.0) {
if (which < RESET_DT || next_time_dump[idump] < 0.0) {
nexttime = input->variable->compute_equal(ivar_dump[idump]);
} else
nexttime = next_time_dump[idump];
@ -703,7 +716,7 @@ void Output::reset_dt()
// since timestep change affects next step
if (next_dump[idump] != ntimestep)
calculate_next_dump(2,idump,update->ntimestep);
calculate_next_dump(RESET_DT,idump,update->ntimestep);
if (dump[idump]->clearstep || var_dump[idump])
next_time_dump_any = MIN(next_time_dump_any,next_dump[idump]);