From f8d06291c9fe73b1f5d377cf067c5ddf1b9bd09d Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 27 Jun 2007 16:47:01 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@685 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 23 ++--- doc/Section_commands.txt | 4 +- doc/displace_atoms.html | 18 ++-- doc/displace_atoms.txt | 18 ++-- doc/displace_box.html | 191 ++++++++++++++++++++++++++++++++++++++ doc/displace_box.txt | 181 ++++++++++++++++++++++++++++++++++++ doc/fix_deform.html | 2 +- doc/fix_deform.txt | 2 +- 8 files changed, 409 insertions(+), 30 deletions(-) create mode 100644 doc/displace_box.html create mode 100644 doc/displace_box.txt diff --git a/doc/Section_commands.html b/doc/Section_commands.html index d03f96a6c9..c3fbef2c7a 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -271,7 +271,8 @@ in the command's documentation.

Actions:

delete_atoms, delete_bonds, -displace_atoms, minimize, +displace_atoms, +displace_box, minimize, run, temper

Miscellaneous: @@ -298,16 +299,16 @@ in the command's documentation. angle_coeffangle_styleatom_modifyatom_stylebond_coeffbond_style boundaryclearcommunicatecomputecompute_modifycreate_atoms create_boxdelete_atomsdelete_bondsdielectricdihedral_coeffdihedral_style -dimensiondipoledisplace_atomsdumpdump_modifyecho -fixfix_modifygroupifimproper_coeffimproper_style -includejumpkspace_modifykspace_stylelabellattice -logmassminimizemin_modifymin_styleneigh_modify -neighbornewtonnextpair_coeffpair_modifypair_style -pair_writeprintprocessorsread_dataread_restartregion -replicatereset_timesteprestartrunrun_styleset -shapeshellspecial_bondstemperthermothermo_modify -thermo_styletimestepuncomputeundumpunfixunits -variablevelocitywrite_restart +dimensiondipoledisplace_atomsdisplace_boxdumpdump_modify +echofixfix_modifygroupifimproper_coeff +improper_styleincludejumpkspace_modifykspace_stylelabel +latticelogmassminimizemin_modifymin_style +neigh_modifyneighbornewtonnextpair_coeffpair_modify +pair_stylepair_writeprintprocessorsread_dataread_restart +regionreplicatereset_timesteprestartrunrun_style +setshapeshellspecial_bondstemperthermo +thermo_modifythermo_styletimestepuncomputeundumpunfix +unitsvariablevelocitywrite_restart

diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 5efd8e093e..e66099f66a 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -268,7 +268,8 @@ Output: Actions: "delete_atoms"_delete_atoms.html, "delete_bonds"_delete_bonds.html, -"displace_atoms"_displace_atoms.html, "minimize"_minimize.html, +"displace_atoms"_displace_atoms.html, +"displace_box"_displace_box.html, "minimize"_minimize.html, "run"_run.html, "temper"_temper.html Miscellaneous: @@ -312,6 +313,7 @@ in the command's documentation. "dimension"_dimension.html, "dipole"_dipole.html, "displace_atoms"_displace_atoms.html, +"displace_box"_displace_box.html, "dump"_dump.html, "dump_modify"_dump_modify.html, "echo"_echo.html, diff --git a/doc/displace_atoms.html b/doc/displace_atoms.html index 985679c2d3..2ae031f132 100644 --- a/doc/displace_atoms.html +++ b/doc/displace_atoms.html @@ -74,18 +74,20 @@ units. Lattice means distance units are in lattice spacings. The lattice command must have been previously used to define the lattice spacing.

+
+

Care should be taken not to move atoms on top of other atoms. After the move, atoms are remapped into the periodic simulation box if needed.

-

Atoms can be moved arbitrarily long distances by this command. -However if the box is non-periodic, this can change the shape of the -simulation box. This is not a problem, except that the mapping of -processors to the simulation box is not changed from its initial 3d -configuration by this command; see the processors -command. Thus, if the box shape changes dramatically, the simulation -may not be as well load-balanced (atoms per processor) as the initial -mapping tried to achieve. +

Atoms can be moved arbitrarily long distances by this command. If the +simulation box is non-periodic, this can change its size or shape. +This is not a problem, except that the mapping of processors to the +simulation box is not changed by this command from its initial 3d +configuration; see the processors command. Thus, if +the box size or shape changes dramatically, the simulation may not be +as well load-balanced (atoms per processor) as the initial mapping +tried to achieve.

Restrictions:

diff --git a/doc/displace_atoms.txt b/doc/displace_atoms.txt index 1e197d505b..26fa1672c4 100644 --- a/doc/displace_atoms.txt +++ b/doc/displace_atoms.txt @@ -66,18 +66,20 @@ units. {Lattice} means distance units are in lattice spacings. The "lattice"_lattice.html command must have been previously used to define the lattice spacing. +:line + Care should be taken not to move atoms on top of other atoms. After the move, atoms are remapped into the periodic simulation box if needed. -Atoms can be moved arbitrarily long distances by this command. -However if the box is non-periodic, this can change the shape of the -simulation box. This is not a problem, except that the mapping of -processors to the simulation box is not changed from its initial 3d -configuration by this command; see the "processors"_processors.html -command. Thus, if the box shape changes dramatically, the simulation -may not be as well load-balanced (atoms per processor) as the initial -mapping tried to achieve. +Atoms can be moved arbitrarily long distances by this command. If the +simulation box is non-periodic, this can change its size or shape. +This is not a problem, except that the mapping of processors to the +simulation box is not changed by this command from its initial 3d +configuration; see the "processors"_processors.html command. Thus, if +the box size or shape changes dramatically, the simulation may not be +as well load-balanced (atoms per processor) as the initial mapping +tried to achieve. [Restrictions:] diff --git a/doc/displace_box.html b/doc/displace_box.html new file mode 100644 index 0000000000..520bba37f5 --- /dev/null +++ b/doc/displace_box.html @@ -0,0 +1,191 @@ + +
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
+ + + + + + +
+ +

displace_box command +

+

Syntax: +

+
displace_box group-ID parameter args ... keyword value ... 
+
+ +

Examples: +

+
displace_box all xy final -2.0 z final 0.0 5.0 units box
+displace_box all x scale 1.1 y volume z volume 
+
+

Description: +

+

Change the volume and/or shape of the simulation box. Orthogonal +simulation boxes have 3 adjustable parameters (x,y,z). Triclinic +(non-orthogonal) simulation boxes have 6 adjustable parameters +(x,y,z,xy,xz,yz). Any or all of them can be adjusted independently +and simultaneously by this command. This fix can be used to expand or +contract a box, or to apply a shear strain to a non-orthogonal box. +

+

Any parameter varied by this command must refer to a periodic +dimension - see the boundary command. For parameters +"xy", "xz", and "yz" this means both affected dimensions must be +periodic, e.g. x and y for "xy". Dimensions not varied by this +command can be periodic or non-periodic. +

+

The size and shape of the initial simulation box are specified by the +create_box or read_data or +read_restart command used to setup the simulation, +or they are the values from the end of the previous run. The +create_box, read data, and +read_restart commands also determine whether the +simulation box is orthogonal or triclinic and their doc pages explain +the meaning of the xy,xz,yz tilt factors. If the displace_box command +changes the xy,xz,yz tilt factors, then the simulation box must be +triclinic, even if its initial tilt factors are 0.0. +

+
+ +

For the x, y, and z parameters, this is the meaning of their +styles and values. +

+

For style final, the final lo and hi box boundaries of a dimension +are specified. The values can be in lattice or box distance units. +See the discsussion of the units keyword below. +

+

For style delta, plus or minus changes in the lo/hi box boundaries +of a dimension are specified. The values can be in lattice or box +distance units. See the discussion of the units keyword below. +

+

For style scale, a multiplicative factor to apply to the box length +of a dimension is specified. For example, if the initial box length +is 10, and the factor is 1.1, then the final box length will be 11. A +factor less than 1.0 means compression. +

+

The volume style changes the specified dimension in such a way that +the box volume remains constant while other box dimensions are changed +explicitly via the styles discussed above. For example, "x scale 1.1 +y scale 1.1 z volume" will shrink the z box length as the x,y box +lengths increase, to keep the volume constant (product of x,y,z +lengths). If "x scale 1.1 z volume" is specified and parameter y is +unspecified, then the z box length will shrink as x increases to keep +the product of x,z lengths constant. If "x scale 1.1 y volume z +volume" is specified, then both the y,z box lengths will shrink as x +increases to keep the volume constant (product of x,y,z lengths). In +this case, the y,z box lengths shrink so as to keep their relative +aspect ratio constant. +

+

For solids or liquids, note that when one dimension of the box is +expanded by this command, it may be physically undesirable to hold the +other 2 box lengths constant (unspecified by this command) since that +implies a density change. Using the volume style for those 2 +dimensions to keep the box volume constant may make more physical +sense, but may also not be correct for materials and potentials whose +Poisson ratio is not 0.5. +

+

For the scale and volume styles, the box length is expanded or +compressed around its mid point. +

+
+ +

For the xy, xz, and yz parameters, this is the meaning of their +styles and values. Note that changing the tilt factors of a triclinic +box does not change its volume. +

+

For style final, the final tilt factor is specified. The value +can be in lattice or box distance units. See the discussion of the +units keyword below. +

+

For style delta, a plus or minus change in the tilt factor is +specified. The value can be in lattice or box distance units. See +the discsussion of the units keyword below. +

+

All of these styles change the xy, xz, yz tilt factors. In LAMMPS, +tilt factors (xy,xz,yz) for triclinic boxes are always bounded by half +the distance of the parallel box length. For example, if xlo = 2 and +xhi = 12, then the x box length is 10 and the xy tilt factor must be +between -5 and 5. Similarly, both xz and yz must be between +-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation, +since if the maximum tilt factor is 5 (as in this example), then +configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all +equivalent. Any tilt factor specified by this command must be within +these limits. +

+
+ +

The remap keyword determines whether atom positions are re-mapped to +the new box. If remap is set to x (the default), atoms in the fix +group are re-mapped; otherwise they are not. If remap is set to +none, then this remapping does not take place. +

+

The units keyword determines the meaning of the distance units used +to define various arguments. A box value selects standard distance +units as defined by the units command, e.g. Angstroms for +units = real or metal. A lattice value means the distance units are +in lattice spacings. The lattice command must have +been previously used to define the lattice spacing. +

+
+ +

The simulation box size or shape can be changed by arbitrarily large +amounts by this command. This is not a problem, except that the +mapping of processors to the simulation box is not changed by this +command from its initial 3d configuration; see the +processors command. Thus, if the box size or shape +changes dramatically, the simulation may not be as well load-balanced +(atoms per processor) as the initial mapping tried to achieve. +

+

Restrictions: +

+

Any box dimension varied by this fix must be periodic. +

+

This command requires inter-processor communication to migrate atoms +once they have moved. This means that your system must be ready to +perform a simulation before using this command (force fields are +setup, atom masses are set, etc). +

+

Related commands: +

+

fix deform +

+

Default: +

+

The option defaults are remap = x and units = lattice. +

+ diff --git a/doc/displace_box.txt b/doc/displace_box.txt new file mode 100644 index 0000000000..9ce44994eb --- /dev/null +++ b/doc/displace_box.txt @@ -0,0 +1,181 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +displace_box command :h3 + +[Syntax:] + +displace_box group-ID parameter args ... keyword value ... :pre + +group-ID = ID of group of atoms to displace :ulb,l +one or more parameter/arg pairs may be appended :l +parameter = {x} or {y} or {z} or {xy} or {xz} or {yz} + {x}, {y}, {z} args = style value(s) + style = {final} or {delta} or {scale} or {volume} + {final} values = lo hi + lo hi = box boundaries at end of run (distance units) + {delta} values = dlo dhi + dlo dhi = change in box boundaries at end of run (distance units) + {scale} values = factor + factor = multiplicative factor for change in box length at end of run + {volume} value = none = adjust this dim to preserve volume of system + {xy}, {xz}, {yz} args = style value + style = {final} or {delta} + {final} value = tilt + tilt = tilt factor at end of run (distance units) + {delta} value = dtilt + dtilt = change in tilt factor at end of run (distance units) :pre + +zero or more keyword/value pairs may be appended to the args :l +keyword = {remap} or {units} :l + {remap} value = {x} or {none} + x = remap coords of atoms in group into deforming box + none = no remapping of coords + {units} value = {lattice} or {box} + lattice = distances are defined in lattice units + box = distances are defined in simulation box units :pre +:ule + +[Examples:] + +displace_box all xy final -2.0 z final 0.0 5.0 units box +displace_box all x scale 1.1 y volume z volume :pre + +[Description:] + +Change the volume and/or shape of the simulation box. Orthogonal +simulation boxes have 3 adjustable parameters (x,y,z). Triclinic +(non-orthogonal) simulation boxes have 6 adjustable parameters +(x,y,z,xy,xz,yz). Any or all of them can be adjusted independently +and simultaneously by this command. This fix can be used to expand or +contract a box, or to apply a shear strain to a non-orthogonal box. + +Any parameter varied by this command must refer to a periodic +dimension - see the "boundary"_boundary.html command. For parameters +"xy", "xz", and "yz" this means both affected dimensions must be +periodic, e.g. x and y for "xy". Dimensions not varied by this +command can be periodic or non-periodic. + +The size and shape of the initial simulation box are specified by the +"create_box"_create_box.html or "read_data"_read_data.html or +"read_restart"_read_restart.html command used to setup the simulation, +or they are the values from the end of the previous run. The +"create_box"_create_box.html, "read data"_read_data.html, and +"read_restart"_read_restart.html commands also determine whether the +simulation box is orthogonal or triclinic and their doc pages explain +the meaning of the xy,xz,yz tilt factors. If the displace_box command +changes the xy,xz,yz tilt factors, then the simulation box must be +triclinic, even if its initial tilt factors are 0.0. + +:line + +For the {x}, {y}, and {z} parameters, this is the meaning of their +styles and values. + +For style {final}, the final lo and hi box boundaries of a dimension +are specified. The values can be in lattice or box distance units. +See the discsussion of the units keyword below. + +For style {delta}, plus or minus changes in the lo/hi box boundaries +of a dimension are specified. The values can be in lattice or box +distance units. See the discussion of the units keyword below. + +For style {scale}, a multiplicative factor to apply to the box length +of a dimension is specified. For example, if the initial box length +is 10, and the factor is 1.1, then the final box length will be 11. A +factor less than 1.0 means compression. + +The {volume} style changes the specified dimension in such a way that +the box volume remains constant while other box dimensions are changed +explicitly via the styles discussed above. For example, "x scale 1.1 +y scale 1.1 z volume" will shrink the z box length as the x,y box +lengths increase, to keep the volume constant (product of x,y,z +lengths). If "x scale 1.1 z volume" is specified and parameter {y} is +unspecified, then the z box length will shrink as x increases to keep +the product of x,z lengths constant. If "x scale 1.1 y volume z +volume" is specified, then both the y,z box lengths will shrink as x +increases to keep the volume constant (product of x,y,z lengths). In +this case, the y,z box lengths shrink so as to keep their relative +aspect ratio constant. + +For solids or liquids, note that when one dimension of the box is +expanded by this command, it may be physically undesirable to hold the +other 2 box lengths constant (unspecified by this command) since that +implies a density change. Using the {volume} style for those 2 +dimensions to keep the box volume constant may make more physical +sense, but may also not be correct for materials and potentials whose +Poisson ratio is not 0.5. + +For the {scale} and {volume} styles, the box length is expanded or +compressed around its mid point. + +:line + +For the {xy}, {xz}, and {yz} parameters, this is the meaning of their +styles and values. Note that changing the tilt factors of a triclinic +box does not change its volume. + +For style {final}, the final tilt factor is specified. The value +can be in lattice or box distance units. See the discussion of the +units keyword below. + +For style {delta}, a plus or minus change in the tilt factor is +specified. The value can be in lattice or box distance units. See +the discsussion of the units keyword below. + +All of these styles change the xy, xz, yz tilt factors. In LAMMPS, +tilt factors (xy,xz,yz) for triclinic boxes are always bounded by half +the distance of the parallel box length. For example, if xlo = 2 and +xhi = 12, then the x box length is 10 and the xy tilt factor must be +between -5 and 5. Similarly, both xz and yz must be between +-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation, +since if the maximum tilt factor is 5 (as in this example), then +configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all +equivalent. Any tilt factor specified by this command must be within +these limits. + +:line + +The {remap} keyword determines whether atom positions are re-mapped to +the new box. If {remap} is set to {x} (the default), atoms in the fix +group are re-mapped; otherwise they are not. If {remap} is set to +{none}, then this remapping does not take place. + +The {units} keyword determines the meaning of the distance units used +to define various arguments. A {box} value selects standard distance +units as defined by the "units"_units.html command, e.g. Angstroms for +units = real or metal. A {lattice} value means the distance units are +in lattice spacings. The "lattice"_lattice.html command must have +been previously used to define the lattice spacing. + +:line + +The simulation box size or shape can be changed by arbitrarily large +amounts by this command. This is not a problem, except that the +mapping of processors to the simulation box is not changed by this +command from its initial 3d configuration; see the +"processors"_processors.html command. Thus, if the box size or shape +changes dramatically, the simulation may not be as well load-balanced +(atoms per processor) as the initial mapping tried to achieve. + +[Restrictions:] + +Any box dimension varied by this fix must be periodic. + +This command requires inter-processor communication to migrate atoms +once they have moved. This means that your system must be ready to +perform a simulation before using this command (force fields are +setup, atom masses are set, etc). + +[Related commands:] + +"fix deform"_fix_deform.html + +[Default:] + +The option defaults are remap = x and units = lattice. diff --git a/doc/fix_deform.html b/doc/fix_deform.html index fa827892f4..7dd214497b 100644 --- a/doc/fix_deform.html +++ b/doc/fix_deform.html @@ -130,7 +130,7 @@ See the discsussion of the units keyword below.

For style delta, plus or minus changes in the lo/hi box boundaries of a dimension are specified. The values can be in lattice or box -distance units. See the discsussion of the units keyword below. +distance units. See the discussion of the units keyword below.

For style scale, a multiplicative factor to apply to the box length of a dimension is specified. For example, if the initial box length diff --git a/doc/fix_deform.txt b/doc/fix_deform.txt index 7b3d1f8ea7..2ea8fa75db 100644 --- a/doc/fix_deform.txt +++ b/doc/fix_deform.txt @@ -119,7 +119,7 @@ See the discsussion of the units keyword below. For style {delta}, plus or minus changes in the lo/hi box boundaries of a dimension are specified. The values can be in lattice or box -distance units. See the discsussion of the units keyword below. +distance units. See the discussion of the units keyword below. For style {scale}, a multiplicative factor to apply to the box length of a dimension is specified. For example, if the initial box length