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recover failing unit tests and whitespace fixes

This commit is contained in:
Axel Kohlmeyer 2021-12-23 15:19:17 -05:00
parent 7018ba65be
commit a653ee6b2c
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GPG Key ID: D9B44E93BF0C375A
5 changed files with 42 additions and 23 deletions
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2
src/EXTRA-DUMP/dump_xtc.cpp
View File

@ -128,7 +128,7 @@ void DumpXTC::init_style()
int idump;
for (idump = 0; idump < output->ndump; idump++)
if (strcmp(id,output->dump[idump]->id) == 0) break;
if (output->mode_dump[idump] == 1)
error->all(FLERR,"Cannot use every/time setting for dump xtc");

4
src/integrate.cpp
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@ -120,7 +120,7 @@ void Integrate::ev_setup()
(1) computes that need energy/virial info on this timestep
(2) time dumps that may need per-atom compute info on this timestep
NOTE: inefficient to add all per-atom eng/virial computes
but don't know which ones the dump needs
but don't know which ones the dump needs
see NOTE in output.cpp
invoke matchstep() on all timestep-dependent computes to clear their arrays
eflag: set any or no bits
@ -140,7 +140,7 @@ void Integrate::ev_set(bigint ntimestep)
int i,flag;
int tdflag = 0;
if (output->any_time_dumps &&
if (output->any_time_dumps &&
output->next_time_dump_any == ntimestep) tdflag = 1;
flag = 0;

40
src/output.cpp
View File

@ -199,9 +199,9 @@ void Output::setup(int memflag)
// (2) and (3) only apply for non-variable dump intervals
// finally, do not write if same snapshot written previously,
// i.e. on last timestep of previous run
int writeflag = 0;
if (last_dump[idump] < 0 && dump[idump]->first_flag == 1) writeflag = 1;
if (mode_dump[idump] == 0) {
@ -209,7 +209,7 @@ void Output::setup(int memflag)
writeflag = 1;
} else {
if (every_time_dump[idump] > 0.0) {
double tcurrent = update->atime +
double tcurrent = update->atime +
(ntimestep - update->atimestep) * update->dt;
double remainder = fmod(tcurrent,every_time_dump[idump]);
if ((remainder < EPSDT*update->dt) ||
@ -234,7 +234,7 @@ void Output::setup(int memflag)
if (writeflag || last_dump[idump] < 0)
calculate_next_dump(0,idump,ntimestep);
// if dump not written now, use addstep_compute_all()
// if dump not written now, use addstep_compute_all()
// since don't know what computes the dump will invoke
if (mode_dump[idump] == 0 &&
@ -354,7 +354,7 @@ void Output::setup(int memflag)
if (next_dump[idump] == ntimestep) {
if (last_dump[idump] == ntimestep) continue;
if (mode_dump[idump] == 0 &&
if (mode_dump[idump] == 0 &&
(dump[idump]->clearstep || var_dump[idump]))
modify->clearstep_compute();
@ -365,7 +365,7 @@ void Output::setup(int memflag)
last_dump[idump] = ntimestep;
calculate_next_dump(1,idump,ntimestep);
if (mode_dump[idump] == 0 &&
if (mode_dump[idump] == 0 &&
(dump[idump]->clearstep || var_dump[idump]))
modify->addstep_compute(next_dump[idump]);
}
@ -490,7 +490,7 @@ void Output::setup(int memflag)
if (which == 0)
next_dump[idump] =
(ntimestep/every_dump[idump])*every_dump[idump] + every_dump[idump];
else if (which == 1)
else if (which == 1)
next_dump[idump] += every_dump[idump];
} else {
@ -507,7 +507,7 @@ void Output::setup(int memflag)
bigint nextdump;
double nexttime;
double tcurrent = update->atime +
double tcurrent = update->atime +
(ntimestep - update->atimestep) * update->dt;
if (every_time_dump[idump] > 0.0) {
@ -517,27 +517,27 @@ void Output::setup(int memflag)
// which = 2: no change to previous nexttime (only timestep has changed)
if (which == 0)
nexttime = static_cast<bigint> (tcurrent/every_time_dump[idump]) *
nexttime = static_cast<bigint> (tcurrent/every_time_dump[idump]) *
every_time_dump[idump] + every_time_dump[idump];
else if (which == 1)
else if (which == 1)
nexttime = next_time_dump[idump] + every_time_dump[idump];
else if (which == 2)
nexttime = next_time_dump[idump];
nextdump = ntimestep +
static_cast<bigint> ((nexttime - tcurrent - EPSDT*update->dt) /
nextdump = ntimestep +
static_cast<bigint> ((nexttime - tcurrent - EPSDT*update->dt) /
update->dt) + 1;
// if delta is too small to reach next timestep, use multiple of delta
if (nextdump == ntimestep) {
double tnext = update->atime +
double tnext = update->atime +
(ntimestep+1 - update->atimestep) * update->dt;
int multiple = static_cast<int>
int multiple = static_cast<int>
((tnext - nexttime) / every_time_dump[idump]);
nexttime = nexttime + (multiple+1)*every_time_dump[idump];
nextdump = ntimestep +
static_cast<bigint> ((nexttime - tcurrent - EPSDT*update->dt) /
nextdump = ntimestep +
static_cast<bigint> ((nexttime - tcurrent - EPSDT*update->dt) /
update->dt) + 1;
}
@ -548,14 +548,14 @@ void Output::setup(int memflag)
if (which < 2 || next_time_dump[idump] < 0.0) {
nexttime = input->variable->compute_equal(ivar_dump[idump]);
} else
} else
nexttime = next_time_dump[idump];
if (nexttime <= tcurrent)
error->all(FLERR,"Dump every/time variable returned a bad time");
nextdump = ntimestep +
static_cast<bigint> ((nexttime - tcurrent - EPSDT*update->dt) /
nextdump = ntimestep +
static_cast<bigint> ((nexttime - tcurrent - EPSDT*update->dt) /
update->dt) + 1;
if (nextdump <= ntimestep)
error->all(FLERR,"Dump every/time variable too small for next timestep");
@ -704,7 +704,7 @@ void Output::reset_dt()
// reset next_dump but do not change next_time_dump, 2 arg for reset_dt()
// do not invoke for a dump already scheduled for this step
// since timestep change affects next step
if (next_dump[idump] != ntimestep)
calculate_next_dump(2,idump,update->ntimestep);

9
unittest/formats/test_dump_atom.cpp
View File

@ -74,6 +74,13 @@ public:
END_HIDE_OUTPUT();
}
void close_dump()
{
BEGIN_HIDE_OUTPUT();
command("undump id");
END_HIDE_OUTPUT();
}
void generate_text_and_binary_dump(std::string text_file, std::string binary_file,
std::string dump_modify_options, int ntimesteps)
{
@ -505,6 +512,7 @@ TEST_F(DumpAtomTest, rerun)
ASSERT_FILE_EXISTS(dump_file);
ASSERT_EQ(count_lines(dump_file), 82);
continue_dump(1);
close_dump();
lmp->output->thermo->evaluate_keyword("pe", &pe_2);
ASSERT_FILE_EXISTS(dump_file);
ASSERT_EQ(count_lines(dump_file), 123);
@ -532,6 +540,7 @@ TEST_F(DumpAtomTest, rerun_bin)
lmp->output->thermo->evaluate_keyword("pe", &pe_1);
ASSERT_FILE_EXISTS(dump_file);
continue_dump(1);
close_dump();
lmp->output->thermo->evaluate_keyword("pe", &pe_2);
ASSERT_FILE_EXISTS(dump_file);
HIDE_OUTPUT([&] {

10
unittest/formats/test_dump_custom.cpp
View File

@ -73,6 +73,13 @@ public:
END_HIDE_OUTPUT();
}
void close_dump()
{
BEGIN_HIDE_OUTPUT();
command("undump id");
END_HIDE_OUTPUT();
}
void generate_text_and_binary_dump(std::string text_file, std::string binary_file,
std::string fields, std::string dump_modify_options,
int ntimesteps)
@ -330,6 +337,7 @@ TEST_F(DumpCustomTest, rerun)
ASSERT_FILE_EXISTS(dump_file);
ASSERT_EQ(count_lines(dump_file), 82);
continue_dump(1);
close_dump();
lmp->output->thermo->evaluate_keyword("pe", &pe_2);
ASSERT_FILE_EXISTS(dump_file);
ASSERT_EQ(count_lines(dump_file), 123);
@ -338,6 +346,7 @@ TEST_F(DumpCustomTest, rerun)
});
lmp->output->thermo->evaluate_keyword("pe", &pe_rerun);
ASSERT_DOUBLE_EQ(pe_1, pe_rerun);
HIDE_OUTPUT([&] {
command(fmt::format("rerun {} first 2 last 2 every 1 post yes dump x y z", dump_file));
});
@ -359,6 +368,7 @@ TEST_F(DumpCustomTest, rerun_bin)
lmp->output->thermo->evaluate_keyword("pe", &pe_1);
ASSERT_FILE_EXISTS(dump_file);
continue_dump(1);
close_dump();
lmp->output->thermo->evaluate_keyword("pe", &pe_2);
ASSERT_FILE_EXISTS(dump_file);
HIDE_OUTPUT([&] {