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Merge pull request lammps#4202 from lammps/dump-triclinic-bug-fix
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Dump triclinic bug fix
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@akohlmey
akohlmey authored Jun 21, 2024
2 parents 13f0e37 + cf2dede commit cfcd2b2
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Showing 3 changed files with 152 additions and 54 deletions.
4 changes: 2 additions & 2 deletions examples/triclinic/dump.8Apr24.general.g++.1
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Original file line number Diff line number Diff line change
Expand Up @@ -7,5 +7,5 @@ ITEM: BOX BOUNDS abc origin pp pp pp
9.9999999999999989e-01 9.9999999999999989e-01 0.0000000000000000e+00 0.0000000000000000e+00
9.9999999999999989e-01 9.9999999999999989e-01 1.0000000000000000e+00 0.0000000000000000e+00
ITEM: ATOMS id type x y z
1 1 0.141421 0.141421 0.1
2 1 0.565685 0.565685 0.3
1 1 0.2 -1.38778e-17 0.1
2 1 0.8 -1.11022e-16 0.3
4 changes: 2 additions & 2 deletions examples/triclinic/dump.8Apr24.general.g++.4
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Original file line number Diff line number Diff line change
Expand Up @@ -7,5 +7,5 @@ ITEM: BOX BOUNDS abc origin pp pp pp
9.9999999999999989e-01 9.9999999999999989e-01 0.0000000000000000e+00 0.0000000000000000e+00
9.9999999999999989e-01 9.9999999999999989e-01 1.0000000000000000e+00 0.0000000000000000e+00
ITEM: ATOMS id type x y z
1 1 0.141421 0.141421 0.1
2 1 0.565685 0.565685 0.3
1 1 0.2 -1.38778e-17 0.1
2 1 0.8 -1.11022e-16 0.3
198 changes: 148 additions & 50 deletions src/dump_custom.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -240,7 +240,7 @@ DumpCustom::~DumpCustom()

void DumpCustom::init_style()
{
// assemble ITEMS: column string from defaults and user values
// assemble ITEMS column string from defaults and user values

delete[] columns;
std::string combined;
Expand Down Expand Up @@ -293,7 +293,7 @@ void DumpCustom::init_style()

domain->boundary_string(boundstr);

// setup function ptrs
// setup function ptrs for writing header and file format

if (binary && domain->triclinic == 0)
header_choice = &DumpCustom::header_binary;
Expand All @@ -312,6 +312,128 @@ void DumpCustom::init_style()
else if (buffer_flag == 1) write_choice = &DumpCustom::write_string;
else write_choice = &DumpCustom::write_lines;

// triclinic_general can be toggled by dump_modify before or between runs
// change any affected pack_choice function ptrs

if (triclinic_general == 0) {
for (int n = 0; n < size_one; n++) {
if (pack_choice[n] == &DumpCustom::pack_x_triclinic_general)
pack_choice[n] = &DumpCustom::pack_x;
else if (pack_choice[n] == &DumpCustom::pack_y_triclinic_general)
pack_choice[n] = &DumpCustom::pack_y;
else if (pack_choice[n] == &DumpCustom::pack_z_triclinic_general)
pack_choice[n] = &DumpCustom::pack_z;
else if (pack_choice[n] == &DumpCustom::pack_xu_triclinic_general) {
if (domain->triclinic) pack_choice[n] = &DumpCustom::pack_xu_triclinic;
else pack_choice[n] == &DumpCustom::pack_xu;
} else if (pack_choice[n] == &DumpCustom::pack_yu_triclinic_general) {
if (domain->triclinic) pack_choice[n] = &DumpCustom::pack_yu_triclinic;
else pack_choice[n] == &DumpCustom::pack_yu;
} else if (pack_choice[n] == &DumpCustom::pack_zu_triclinic_general) {
if (domain->triclinic) pack_choice[n] = &DumpCustom::pack_zu_triclinic;
else pack_choice[n] == &DumpCustom::pack_zu;
}

else if (pack_choice[n] == &DumpCustom::pack_vx_triclinic_general)
pack_choice[n] = &DumpCustom::pack_vx;
else if (pack_choice[n] == &DumpCustom::pack_vy_triclinic_general)
pack_choice[n] = &DumpCustom::pack_vy;
else if (pack_choice[n] == &DumpCustom::pack_vz_triclinic_general)
pack_choice[n] = &DumpCustom::pack_vz;
else if (pack_choice[n] == &DumpCustom::pack_fx_triclinic_general)
pack_choice[n] = &DumpCustom::pack_fx;
else if (pack_choice[n] == &DumpCustom::pack_fy_triclinic_general)
pack_choice[n] = &DumpCustom::pack_fy;
else if (pack_choice[n] == &DumpCustom::pack_fz_triclinic_general)
pack_choice[n] = &DumpCustom::pack_fz;

else if (pack_choice[n] == &DumpCustom::pack_mux_triclinic_general)
pack_choice[n] = &DumpCustom::pack_mux;
else if (pack_choice[n] == &DumpCustom::pack_muy_triclinic_general)
pack_choice[n] = &DumpCustom::pack_muy;
else if (pack_choice[n] == &DumpCustom::pack_muz_triclinic_general)
pack_choice[n] = &DumpCustom::pack_muz;

else if (pack_choice[n] == &DumpCustom::pack_omegax_triclinic_general)
pack_choice[n] = &DumpCustom::pack_omegax;
else if (pack_choice[n] == &DumpCustom::pack_omegay_triclinic_general)
pack_choice[n] = &DumpCustom::pack_omegay;
else if (pack_choice[n] == &DumpCustom::pack_omegaz_triclinic_general)
pack_choice[n] = &DumpCustom::pack_omegaz;
else if (pack_choice[n] == &DumpCustom::pack_angmomx_triclinic_general)
pack_choice[n] = &DumpCustom::pack_angmomx;
else if (pack_choice[n] == &DumpCustom::pack_angmomy_triclinic_general)
pack_choice[n] = &DumpCustom::pack_angmomy;
else if (pack_choice[n] == &DumpCustom::pack_angmomz_triclinic_general)
pack_choice[n] = &DumpCustom::pack_angmomz;
else if (pack_choice[n] == &DumpCustom::pack_tqx_triclinic_general)
pack_choice[n] = &DumpCustom::pack_tqx;
else if (pack_choice[n] == &DumpCustom::pack_tqy_triclinic_general)
pack_choice[n] = &DumpCustom::pack_tqy;
else if (pack_choice[n] == &DumpCustom::pack_tqz_triclinic_general)
pack_choice[n] = &DumpCustom::pack_tqz;
}
}

if (triclinic_general == 1) {
for (int n = 0; n < size_one; n++) {
if (pack_choice[n] == &DumpCustom::pack_x)
pack_choice[n] = &DumpCustom::pack_x_triclinic_general;
else if (pack_choice[n] == &DumpCustom::pack_y)
pack_choice[n] = &DumpCustom::pack_y_triclinic_general;
else if (pack_choice[n] == &DumpCustom::pack_z)
pack_choice[n] = &DumpCustom::pack_z_triclinic_general;
else if (pack_choice[n] == &DumpCustom::pack_xu ||
pack_choice[n] == &DumpCustom::pack_xu_triclinic)
pack_choice[n] = &DumpCustom::pack_xu_triclinic_general;
else if (pack_choice[n] == &DumpCustom::pack_yu ||
pack_choice[n] == &DumpCustom::pack_yu_triclinic)
pack_choice[n] = &DumpCustom::pack_yu_triclinic_general;
else if (pack_choice[n] == &DumpCustom::pack_zu ||
pack_choice[n] == &DumpCustom::pack_zu_triclinic)
pack_choice[n] = &DumpCustom::pack_zu_triclinic_general;

else if (pack_choice[n] == &DumpCustom::pack_vx)
pack_choice[n] = &DumpCustom::pack_vx_triclinic_general;
else if (pack_choice[n] == &DumpCustom::pack_vy)
pack_choice[n] = &DumpCustom::pack_vy_triclinic_general;
else if (pack_choice[n] == &DumpCustom::pack_vz)
pack_choice[n] = &DumpCustom::pack_vz_triclinic_general;
else if (pack_choice[n] == &DumpCustom::pack_fx)
pack_choice[n] = &DumpCustom::pack_fx_triclinic_general;
else if (pack_choice[n] == &DumpCustom::pack_fy)
pack_choice[n] = &DumpCustom::pack_fy_triclinic_general;
else if (pack_choice[n] == &DumpCustom::pack_fz)
pack_choice[n] = &DumpCustom::pack_fz_triclinic_general;

else if (pack_choice[n] == &DumpCustom::pack_mux)
pack_choice[n] = &DumpCustom::pack_mux_triclinic_general;
else if (pack_choice[n] == &DumpCustom::pack_muy)
pack_choice[n] = &DumpCustom::pack_muy_triclinic_general;
else if (pack_choice[n] == &DumpCustom::pack_muz)
pack_choice[n] = &DumpCustom::pack_muz_triclinic_general;

else if (pack_choice[n] == &DumpCustom::pack_omegax)
pack_choice[n] = &DumpCustom::pack_omegax_triclinic_general;
else if (pack_choice[n] == &DumpCustom::pack_omegay)
pack_choice[n] = &DumpCustom::pack_omegay_triclinic_general;
else if (pack_choice[n] == &DumpCustom::pack_omegaz)
pack_choice[n] = &DumpCustom::pack_omegaz_triclinic_general;
else if (pack_choice[n] == &DumpCustom::pack_angmomx)
pack_choice[n] = &DumpCustom::pack_angmomx_triclinic_general;
else if (pack_choice[n] == &DumpCustom::pack_angmomy)
pack_choice[n] = &DumpCustom::pack_angmomy_triclinic_general;
else if (pack_choice[n] == &DumpCustom::pack_angmomz)
pack_choice[n] = &DumpCustom::pack_angmomz_triclinic_general;
else if (pack_choice[n] == &DumpCustom::pack_tqx)
pack_choice[n] = &DumpCustom::pack_tqx_triclinic_general;
else if (pack_choice[n] == &DumpCustom::pack_tqy)
pack_choice[n] = &DumpCustom::pack_tqy_triclinic_general;
else if (pack_choice[n] == &DumpCustom::pack_tqz)
pack_choice[n] = &DumpCustom::pack_tqz_triclinic_general;
}
}

// find current ptr for each compute,fix,variable and custom atom property
// check that fix frequency is acceptable

Expand Down Expand Up @@ -1342,16 +1464,13 @@ int DumpCustom::parse_fields(int narg, char **arg)
vtype[iarg] = Dump::DOUBLE;

} else if (strcmp(arg[iarg],"x") == 0) {
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_x_triclinic_general;
else pack_choice[iarg] = &DumpCustom::pack_x;
pack_choice[iarg] = &DumpCustom::pack_x;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"y") == 0) {
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_y_triclinic_general;
else pack_choice[iarg] = &DumpCustom::pack_y;
pack_choice[iarg] = &DumpCustom::pack_y;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"z") == 0) {
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_z_triclinic_general;
else pack_choice[iarg] = &DumpCustom::pack_z;
pack_choice[iarg] = &DumpCustom::pack_z;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"xs") == 0) {
if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_xs_triclinic;
Expand All @@ -1366,18 +1485,15 @@ int DumpCustom::parse_fields(int narg, char **arg)
else pack_choice[iarg] = &DumpCustom::pack_zs;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"xu") == 0) {
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_xu_triclinic_general;
else if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_xu_triclinic;
if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_xu_triclinic;
else pack_choice[iarg] = &DumpCustom::pack_xu;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"yu") == 0) {
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_yu_triclinic_general;
else if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_yu_triclinic;
if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_yu_triclinic;
else pack_choice[iarg] = &DumpCustom::pack_yu;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"zu") == 0) {
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_zu_triclinic_general;
else if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_zu_triclinic;
if (domain->triclinic) pack_choice[iarg] = &DumpCustom::pack_zu_triclinic;
else pack_choice[iarg] = &DumpCustom::pack_zu;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"xsu") == 0) {
Expand All @@ -1404,28 +1520,22 @@ int DumpCustom::parse_fields(int narg, char **arg)
vtype[iarg] = Dump::INT;

} else if (strcmp(arg[iarg],"vx") == 0) {
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_vx_triclinic_general;
else pack_choice[iarg] = &DumpCustom::pack_vx;
pack_choice[iarg] = &DumpCustom::pack_vx;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"vy") == 0) {
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_vy_triclinic_general;
else pack_choice[iarg] = &DumpCustom::pack_vy;
pack_choice[iarg] = &DumpCustom::pack_vy;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"vz") == 0) {
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_vz_triclinic_general;
else pack_choice[iarg] = &DumpCustom::pack_vz;
pack_choice[iarg] = &DumpCustom::pack_vz;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"fx") == 0) {
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_fx_triclinic_general;
else pack_choice[iarg] = &DumpCustom::pack_fx;
pack_choice[iarg] = &DumpCustom::pack_fx;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"fy") == 0) {
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_fy_triclinic_general;
else pack_choice[iarg] = &DumpCustom::pack_fy;
pack_choice[iarg] = &DumpCustom::pack_fy;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"fz") == 0) {
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_fz_triclinic_general;
else pack_choice[iarg] = &DumpCustom::pack_fz;
pack_choice[iarg] = &DumpCustom::pack_fz;
vtype[iarg] = Dump::DOUBLE;

} else if (strcmp(arg[iarg],"q") == 0) {
Expand All @@ -1437,20 +1547,17 @@ int DumpCustom::parse_fields(int narg, char **arg)
} else if (strcmp(arg[iarg],"mux") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_mux_triclinic_general;
else pack_choice[iarg] = &DumpCustom::pack_mux;
pack_choice[iarg] = &DumpCustom::pack_mux;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"muy") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_muy_triclinic_general;
else pack_choice[iarg] = &DumpCustom::pack_muy;
pack_choice[iarg] = &DumpCustom::pack_muy;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"muz") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_muz_triclinic_general;
else pack_choice[iarg] = &DumpCustom::pack_muz;
pack_choice[iarg] = &DumpCustom::pack_muz;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"mu") == 0) {
if (!atom->mu_flag)
Expand All @@ -1471,58 +1578,49 @@ int DumpCustom::parse_fields(int narg, char **arg)
} else if (strcmp(arg[iarg],"omegax") == 0) {
if (!atom->omega_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_omegax_triclinic_general;
else pack_choice[iarg] = &DumpCustom::pack_omegax;
pack_choice[iarg] = &DumpCustom::pack_omegax;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"omegay") == 0) {
if (!atom->omega_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_omegay_triclinic_general;
else pack_choice[iarg] = &DumpCustom::pack_omegay;
pack_choice[iarg] = &DumpCustom::pack_omegay;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"omegaz") == 0) {
if (!atom->omega_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_omegaz_triclinic_general;
else pack_choice[iarg] = &DumpCustom::pack_omegaz;
pack_choice[iarg] = &DumpCustom::pack_omegaz;
vtype[iarg] = Dump::DOUBLE;

} else if (strcmp(arg[iarg],"angmomx") == 0) {
if (!atom->angmom_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_angmomx_triclinic_general;
else pack_choice[iarg] = &DumpCustom::pack_angmomx;
pack_choice[iarg] = &DumpCustom::pack_angmomx;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"angmomy") == 0) {
if (!atom->angmom_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_angmomy_triclinic_general;
else pack_choice[iarg] = &DumpCustom::pack_angmomy;
pack_choice[iarg] = &DumpCustom::pack_angmomy;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"angmomz") == 0) {
if (!atom->angmom_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_angmomz_triclinic_general;
else pack_choice[iarg] = &DumpCustom::pack_angmomz;
pack_choice[iarg] = &DumpCustom::pack_angmomz;
vtype[iarg] = Dump::DOUBLE;

} else if (strcmp(arg[iarg],"tqx") == 0) {
if (!atom->torque_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_tqx_triclinic_general;
else pack_choice[iarg] = &DumpCustom::pack_tqx;
pack_choice[iarg] = &DumpCustom::pack_tqx;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"tqy") == 0) {
if (!atom->torque_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_tqy_triclinic_general;
else pack_choice[iarg] = &DumpCustom::pack_tqy;
pack_choice[iarg] = &DumpCustom::pack_tqy;
vtype[iarg] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"tqz") == 0) {
if (!atom->torque_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
if (triclinic_general) pack_choice[iarg] = &DumpCustom::pack_tqz_triclinic_general;
else pack_choice[iarg] = &DumpCustom::pack_tqz;
pack_choice[iarg] = &DumpCustom::pack_tqz;
vtype[iarg] = Dump::DOUBLE;

// compute or fix or variable or custom vector/array
Expand Down

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