diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index 6bc1bb8b3e..20460259ec 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -80,7 +80,7 @@ Syntax value = numeric value to compare to, or LAST these 3 args can be replaced by the word "none" to turn off thresholding *time* arg = *yes* or *no* - *triclinic/general* arg = none + *triclinic/general* arg = *yes* or *no* *units* arg = *yes* or *no* *unwrap* arg = *yes* or *no* @@ -815,7 +815,7 @@ threshold criterion is met. Otherwise it is not met. .. note:: - For style *custom*, the *triclinic/general* keyword alters dump + For style *custom*, the *triclinic/general* keyword can alter dump output for general triclinic simulation boxes and their atoms. See the :doc:`dump ` command for details of how this changes the format of dump file snapshots. The thresh keyword may access @@ -850,23 +850,25 @@ The default setting is *no*\ . ---------- The *triclinic/general* keyword only applies to the dump *atom* and -*custom* styles. It can only be used if the simulation box was -created as a general triclinic box. See the :doc:`Howto_triclinic -` doc page for a detailed explanation of orthogonal, -restricted triclinic, and general triclinic simulation boxes. +*custom* styles. It can only be used with a value of *yes* if the +simulation box was created as a general triclinic box. See the +:doc:`Howto_triclinic ` doc page for a detailed +explanation of orthogonal, restricted triclinic, and general triclinic +simulation boxes. -If this keyword is used, the box information at the beginning of each -snapshot will include information about the 3 arbitrary edge vectors -**A**, **B**, **C** that define the general triclinic box as well as -their origin. The format is described on the :doc:`dump ` doc -page. +If this keyword is used with a value of *yes*, the box information at +the beginning of each snapshot will include information about the 3 +arbitrary edge vectors **A**, **B**, **C** that define the general +triclinic box as well as their origin. The format is described on the +:doc:`dump ` doc page. -The coordinates of each atom will be output as values in (or near) the -general triclinic box. Likewise, per-atom vector quantities such as -velocity, omega, dipole moment, etc will have orientations consistent -with the general triclinic box, meaning they will be rotated relative -to the standard xyz coordinate axes. See the :doc:`dump ` doc -page for a full list of which dump attributes this affects. +The coordinates of each atom will likewise be output as values in (or +near) the general triclinic box. Likewise, per-atom vector quantities +such as velocity, omega, dipole moment, etc will have orientations +consistent with the general triclinic box, meaning they will be +rotated relative to the standard xyz coordinate axes. See the +:doc:`dump ` doc page for a full list of which dump attributes +this affects. ---------- diff --git a/doc/src/thermo_modify.rst b/doc/src/thermo_modify.rst index 5eadf2fa10..dcbe313508 100644 --- a/doc/src/thermo_modify.rst +++ b/doc/src/thermo_modify.rst @@ -32,7 +32,7 @@ Syntax *or* a thermo keyword or reference to compute, fix, property or variable. *temp* value = compute ID that calculates a temperature *press* value = compute ID that calculates a pressure - *triclinic/general* arg = none + *triclinic/general* arg = *yes* or *no* Examples @@ -242,16 +242,18 @@ command, thermo output uses a default compute for pressure with ID = keyword, then the new pressure compute specified by the *press* keyword will be unaffected by the *temp* setting. -The *triclinic/general* keyword can only be used if the simulation box -was created as a general triclinic box. See the :doc:`Howto_triclinic -` doc page for a detailed explanation of orthogonal, -restricted triclinic, and general triclinic simulation boxes. +The *triclinic/general* keyword can only be used with a value of *yes* +if the simulation box was created as a general triclinic box. See the +:doc:`Howto_triclinic ` doc page for a detailed +explanation of orthogonal, restricted triclinic, and general triclinic +simulation boxes. -If this keyword is used, the output of the simulation box edge vectors -and the pressure tensor components for the system are affected. These -are specified by the *avec,bvec,cvec* and *pxx,pyy,pzz,pxy,pxz,pyz* -keywords of the :doc:`thermo_style ` command. See the -:doc:`thermo_style ` doc page for details. +If this keyword is *yes*, the output of the simulation box edge +vectors and the pressure tensor components for the system are +affected. These are specified by the *avec,bvec,cvec* and +*pxx,pyy,pzz,pxy,pxz,pyz* keywords of the :doc:`thermo_style +` command. See the :doc:`thermo_style ` +doc page for details. Restrictions """""""""""" @@ -266,8 +268,9 @@ Default """"""" The option defaults are lost = error, warn = 100, norm = yes for unit -style of *lj*, norm = no for unit style of *real* and *metal*, -flush = no, and temp/press = compute IDs defined by thermo_style. +style of *lj*, norm = no for unit style of *real* and *metal*, flush = +no, temp/press = compute IDs defined by thermo_style, and +triclinic/general = no. The defaults for the line and format options depend on the thermo style. For styles "one" and "custom", the line and format defaults are "one", diff --git a/examples/README b/examples/README index f76dced3e4..c2166a0d20 100644 --- a/examples/README +++ b/examples/README @@ -115,7 +115,7 @@ tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si template: examples for using atom_style template and comparing to atom style molecular tersoff: regression test input for Tersoff variants threebody: regression test input for a variety of threebody potentials -triclinic: general and restricted triclinic examples +triclinic: general triclinic simulation box examples ttm: two-temeperature model examples vashishta: models using the Vashishta potential voronoi: Voronoi tesselation via compute voronoi/atom command diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index 6e7ff619b6..fb07efd561 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -1762,14 +1762,6 @@ int DumpCustom::modify_param(int narg, char **arg) return 2; } - if (strcmp(arg[0],"triclinic/general") == 0) { - triclinic_general = 1; - if (triclinic_general && !domain->triclinic_general) - error->all(FLERR,"Dump_modify triclinic/general cannot be used " - "if simulation box is not general triclinic"); - return 1; - } - if (strcmp(arg[0],"triclinic/general") == 0) { if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); triclinic_general = utils::logical(FLERR,arg[1],false,lmp); diff --git a/src/write_data.cpp b/src/write_data.cpp index f62b49c9b2..bc6f1773d4 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -338,7 +338,7 @@ void WriteData::header() domain->bvec[0],domain->bvec[1],domain->bvec[2], domain->cvec[0],domain->cvec[1],domain->cvec[2]); fmt::print(fp,"{} {} {} abc origin\n", - domain->boxlo[0],domain->boxlo[1],domain->boxhi[2]); + domain->boxlo[0],domain->boxlo[1],domain->boxlo[2]); } }