Only information for atoms in the specified group is dumped. The dump_modify thresh and region commands can also @@ -119,7 +119,7 @@ options; see details below.
As described below, the filename determines the kind of output (text or binary or gzipped, one big file or one per timestep, one big file -or one per processor). +or multiple smaller files).
IMPORTANT NOTE: Because periodic boundary conditions are enforced only on timesteps when neighbor lists are rebuilt, the coordinates of an @@ -134,7 +134,7 @@ if the atom_modify sort option is on, which it by default. In this case atoms are re-ordered periodically during a simulation, due to spatial sorting. It is also true when running in parallel, because data for a single snapshot is collected from -multiple processors. +multiple processors, each of which owns a subset of the atoms.
For the atom, custom, cfg, and local styles, sorting is off by default. For the dcd, xtc, xyz, and molfile styles, sorting by @@ -293,11 +293,12 @@ from using the (numerical) atom type to an element name (or some other label). This will help many visualization programs to guess bonds and colors.
-Note that atom, custom, dcd, xtc, and xyz style dump files can -be read directly by VMD (a popular -molecular viewing program). See Section tools -of the manual and the tools/lmp2vmd/README.txt file for more information -about support in VMD for reading and visualizing LAMMPS dump files. +
Note that atom, custom, dcd, xtc, and xyz style dump files +can be read directly by VMD, a +popular molecular viewing program. See Section +tools of the manual and the +tools/lmp2vmd/README.txt file for more information about support in +VMD for reading and visualizing LAMMPS dump files.
If a "%" character appears in the filename, then each of P processors writes a portion of the dump file, and the "%" character is replaced diff --git a/doc/dump.txt b/doc/dump.txt index 9bb80f45bc..05fb34b487 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -97,8 +97,8 @@ timesteps in one of several styles. The {image} style is the exception; it creates a JPG or PPM image file of the atom configuration every N timesteps, as discussed on the "dump image"_dump_image.html doc page. The timesteps on which dump output -is written can also be controlled by a variable. See the "dump_modify -every"_dump_modify.html command. +is written can also be controlled by a variable; see the "dump_modify +every"_dump_modify.html command for details. Only information for atoms in the specified group is dumped. The "dump_modify thresh and region"_dump_modify.html commands can also @@ -107,7 +107,7 @@ options; see details below. As described below, the filename determines the kind of output (text or binary or gzipped, one big file or one per timestep, one big file -or one per processor). +or multiple smaller files). IMPORTANT NOTE: Because periodic boundary conditions are enforced only on timesteps when neighbor lists are rebuilt, the coordinates of an @@ -122,7 +122,7 @@ if the "atom_modify sort"_atom_modify.html option is on, which it is by default. In this case atoms are re-ordered periodically during a simulation, due to spatial sorting. It is also true when running in parallel, because data for a single snapshot is collected from -multiple processors. +multiple processors, each of which owns a subset of the atoms. For the {atom}, {custom}, {cfg}, and {local} styles, sorting is off by default. For the {dcd}, {xtc}, {xyz}, and {molfile} styles, sorting by @@ -281,11 +281,12 @@ from using the (numerical) atom type to an element name (or some other label). This will help many visualization programs to guess bonds and colors. -Note that {atom}, {custom}, {dcd}, {xtc}, and {xyz} style dump files can -be read directly by "VMD"_http://www.ks.uiuc.edu/Research/vmd (a popular -molecular viewing program). See "Section tools"_Section_tools.html#vmd -of the manual and the tools/lmp2vmd/README.txt file for more information -about support in VMD for reading and visualizing LAMMPS dump files. +Note that {atom}, {custom}, {dcd}, {xtc}, and {xyz} style dump files +can be read directly by "VMD"_http://www.ks.uiuc.edu/Research/vmd, a +popular molecular viewing program. See "Section +tools"_Section_tools.html#vmd of the manual and the +tools/lmp2vmd/README.txt file for more information about support in +VMD for reading and visualizing LAMMPS dump files. :line @@ -318,7 +319,7 @@ tmp.dump.20000, etc. This option is not available for the {dcd} and {xtc} styles. Note that the "dump_modify pad"_dump_modify.html command can be used to insure all timestep numbers are the same length (e.g. 00010), which can make it easier to read a series of dump files -in order by some post-processing tools. +in order with some post-processing tools. If a "%" character appears in the filename, then each of P processors writes a portion of the dump file, and the "%" character is replaced diff --git a/doc/dump_modify.html b/doc/dump_modify.html index c925654a84..41db88ccb1 100644 --- a/doc/dump_modify.html +++ b/doc/dump_modify.html @@ -99,10 +99,10 @@ color = name of color for box lines color args = name R G B name = name of color - R,G,B = red/green/blue numeric values from 0.0 to 1.0 - + R,G,B = red/green/blue numeric values from 0.0 to 1.0 framerate arg = fps - fps = frames per second for movie + fps = frames per second for movie +
Examples: @@ -245,6 +245,8 @@ the first two fields (atom id and type) are not actually written into the CFG file, though you must include formats for them in the format string.
+The fileper keyword is documented below with the nfile keyword.
The label keyword applies only to the dump local style. When -it writes local informatoin, such as bond or angle topology +it writes local information, such as bond or angle topology to a dump file, it will use the specified label to format the header. By default this includes 2 lines:
@@ -359,7 +361,7 @@ cost, as well as memory, versus unsorted output.The thresh keyword only applies to the dump custom, cfg, -image, and mvoie styles. Multiple thresholds can be specified. +image, and movie styles. Multiple thresholds can be specified. Specifying "none" turns off all threshold criteria. If thresholds are specified, only atoms whose attributes meet all the threshold criteria are written to the dump file or included in the image. The possible diff --git a/doc/dump_modify.txt b/doc/dump_modify.txt index dca28fdb2d..72208a701d 100644 --- a/doc/dump_modify.txt +++ b/doc/dump_modify.txt @@ -89,9 +89,9 @@ keyword = {acolor} or {adiam} or {amap} or {bcolor} or {bdiam} or {backcolor} or color = name of color for box lines {color} args = name R G B name = name of color - R,G,B = red/green/blue numeric values from 0.0 to 1.0 :pre + R,G,B = red/green/blue numeric values from 0.0 to 1.0 {framerate} arg = fps - fps = frames per second for movie + fps = frames per second for movie :pre :ule [Examples:] @@ -233,6 +233,8 @@ the first two fields (atom id and type) are not actually written into the CFG file, though you must include formats for them in the format string. +:line + The {fileper} keyword is documented below with the {nfile} keyword. :line @@ -250,7 +252,7 @@ attributes in the dump command itself. :line The {label} keyword applies only to the dump {local} style. When -it writes local informatoin, such as bond or angle topology +it writes local information, such as bond or angle topology to a dump file, it will use the specified {label} to format the header. By default this includes 2 lines: @@ -347,7 +349,7 @@ cost, as well as memory, versus unsorted output. :line The {thresh} keyword only applies to the dump {custom}, {cfg}, -{image}, and {mvoie} styles. Multiple thresholds can be specified. +{image}, and {movie} styles. Multiple thresholds can be specified. Specifying "none" turns off all threshold criteria. If thresholds are specified, only atoms whose attributes meet all the threshold criteria are written to the dump file or included in the image. The possible diff --git a/doc/neb.html b/doc/neb.html index 2ef59a5210..fdaec0f976 100644 --- a/doc/neb.html +++ b/doc/neb.html @@ -71,11 +71,11 @@ for further discussion. there to be one processor per replica.
IMPORTANT NOTE: As explained below, a NEB calculation perfoms a -damped-dynamics minimization across all the replicas. This uses +damped-dynamics minimization across all the replicas. This will use whatever timestep you have defined in your input script, via the -timestep command. You may get faster convergence if -you use a larger timestep than you would normally use for dynamics -with the same system. +timestep command. You may get faster convergence for +a NEB calculation if you use a larger timestep than you would normally +use for dynamics with the same system.
When a NEB calculation is performed, it is assumed that each replica is running the same system, though LAMMPS does not check for this. diff --git a/doc/neb.txt b/doc/neb.txt index 68979b5858..b2eaf11ac8 100644 --- a/doc/neb.txt +++ b/doc/neb.txt @@ -61,11 +61,11 @@ IMPORTANT NOTE: The current NEB implementation in LAMMPS only allows there to be one processor per replica. IMPORTANT NOTE: As explained below, a NEB calculation perfoms a -damped-dynamics minimization across all the replicas. This uses +damped-dynamics minimization across all the replicas. This will use whatever timestep you have defined in your input script, via the -"timestep"_timestep.html command. You may get faster convergence if -you use a larger timestep than you would normally use for dynamics -with the same system. +"timestep"_timestep.html command. You may get faster convergence for +a NEB calculation if you use a larger timestep than you would normally +use for dynamics with the same system. When a NEB calculation is performed, it is assumed that each replica is running the same system, though LAMMPS does not check for this. diff --git a/doc/variable.html b/doc/variable.html index 9d59274487..74f9e31214 100644 --- a/doc/variable.html +++ b/doc/variable.html @@ -418,8 +418,8 @@ would occur with the default precedence.
IMPORTANT NOTE: Because a unary minus is higher precedence than exponentiation, the formula "-2^2" will evaluate to 4, not -4. This convention is compatible with some programming languages, but not -others. This behavior can be overridden with parenthesis; the formula -"-(2^2)" will evaluate to -4. +others. As mentioned, this behavior can be easily overridden with +parenthesis; the formula "-(2^2)" will evaluate to -4.
The 6 relational operators return either a 1.0 or 0.0 depending on whether the relationship between x and y is TRUE or FALSE. For diff --git a/doc/variable.txt b/doc/variable.txt index ed65e836a7..721d4845f7 100644 --- a/doc/variable.txt +++ b/doc/variable.txt @@ -418,8 +418,8 @@ would occur with the default precedence. IMPORTANT NOTE: Because a unary minus is higher precedence than exponentiation, the formula "-2^2" will evaluate to 4, not -4. This convention is compatible with some programming languages, but not -others. This behavior can be overridden with parenthesis; the formula -"-(2^2)" will evaluate to -4. +others. As mentioned, this behavior can be easily overridden with +parenthesis; the formula "-(2^2)" will evaluate to -4. The 6 relational operators return either a 1.0 or 0.0 depending on whether the relationship between x and y is TRUE or FALSE. For