temp = temperature of each chunk kecom = kinetic energy of each chunk based on velocity of center of mass - internal = internal kinetic energy of each chunk -zero or more keyword/value pairs may be appended + internal = internal kinetic energy of each chunk ++
The temperature is calculated by the formula KE = DOF k T, where KE = -total kinetic energy of all atoms both in the group and assigned to -chunks (sum of 1/2 m v^2), DOF = the total number of degrees of -freedom for those atoms, k = Boltzmann constant, and T = temperature. +total kinetic energy of all atoms assigned to chunks (sum of 1/2 m +v^2), DOF = the total number of degrees of freedom for those atoms, k += Boltzmann constant, and T = temperature.
The DOF is calculated as N*adof + Nchunk*cdof, where N = number of atoms contributing to the KE, adof = degrees of freedom per atom, and @@ -133,25 +134,26 @@ concept is somewhat ill-defined. In some cases, you can use the adof and cdof keywords to adjust the calculated degress of freedom appropriately, as explained below.
-Note that this compute and the fix ave/chunk temp -command can calculate different things. This compute calculates the -temperature for each chunk for a single snapshot. Fix ave/chunk can -do that but can time average those values over many snapshots, or it -can compute a temperature as if the atoms in the chunk on different -timesteps were collected together as one set of atoms to calculate -their temperature. This compute allows the center-of-mass velocity of -each chunk to be subtracted before calculating the temperature; fix -ave/chunk does not. +
Note that the per-chunk temperature calulated by this compute and the +fix ave/chunk temp command can be different. +This compute calculates the temperature for each chunk for a single +snapshot. Fix ave/chunk can do that but can also time average those +values over many snapshots, or it can compute a temperature as if the +atoms in the chunk on different timesteps were collected together as +one set of atoms to calculate their temperature. This compute allows +the center-of-mass velocity of each chunk to be subtracted before +calculating the temperature; fix ave/chunk does not.
-Note that only atoms in the specified group contribute to the -calculation. The compute chunk/atom command -defines its own group; atoms will have a chunk ID = 0 if they are not -in that group, signifying they are not assigned to a chunk, and will -thus also not contribute to this calculation. You can specify the -"all" group for this command if you simply want to include atoms with -non-zero chunk IDs. +
IMPORTANT NOTE: Only atoms in the specified group contribute to the +calculations performed by this compute. The compute +chunk/atom command defines its own group; +atoms will have a chunk ID = 0 if they are not in that group, +signifying they are not assigned to a chunk, and will thus also not +contribute to this calculation. You can specify the "all" group for +this command if you simply want to include atoms with non-zero chunk +IDs.
-The simplest way to output the pre-chunk results of the compute +
The simplest way to output the per-chunk results of the compute temp/chunk calculation to a file is to use the fix ave/time command, for example:
diff --git a/doc/compute_temp_chunk.txt b/doc/compute_temp_chunk.txt index fe066e9f1a..c98ebb8db7 100644 --- a/doc/compute_temp_chunk.txt +++ b/doc/compute_temp_chunk.txt @@ -15,11 +15,11 @@ compute ID group-ID temp/chunk chunkID value1 value2 ... keyword value ... :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l temp/chunk = style name of this compute command :l chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l -zero or more values can be listed :l +zero or more values can be listed as value1,value2,etc :l value = {temp} or {kecom} or {internal} :l temp = temperature of each chunk kecom = kinetic energy of each chunk based on velocity of center of mass - internal = internal kinetic energy of each chunk + internal = internal kinetic energy of each chunk :pre zero or more keyword/value pairs may be appended :l keyword = {com} or {bias} or {adof} or {cdof} :l {com} value = {yes} or {no} @@ -58,9 +58,9 @@ defined and examples of how they can be used to measure properties of a system. The temperature is calculated by the formula KE = DOF k T, where KE = -total kinetic energy of all atoms both in the group and assigned to -chunks (sum of 1/2 m v^2), DOF = the total number of degrees of -freedom for those atoms, k = Boltzmann constant, and T = temperature. +total kinetic energy of all atoms assigned to chunks (sum of 1/2 m +v^2), DOF = the total number of degrees of freedom for those atoms, k += Boltzmann constant, and T = temperature. The DOF is calculated as N*adof + Nchunk*cdof, where N = number of atoms contributing to the KE, adof = degrees of freedom per atom, and @@ -122,25 +122,26 @@ concept is somewhat ill-defined. In some cases, you can use the {adof} and {cdof} keywords to adjust the calculated degress of freedom appropriately, as explained below. -Note that this compute and the "fix ave/chunk temp"_fix_ave_chunk.html -command can calculate different things. This compute calculates the -temperature for each chunk for a single snapshot. Fix ave/chunk can -do that but can time average those values over many snapshots, or it -can compute a temperature as if the atoms in the chunk on different -timesteps were collected together as one set of atoms to calculate -their temperature. This compute allows the center-of-mass velocity of -each chunk to be subtracted before calculating the temperature; fix -ave/chunk does not. +Note that the per-chunk temperature calulated by this compute and the +"fix ave/chunk temp"_fix_ave_chunk.html command can be different. +This compute calculates the temperature for each chunk for a single +snapshot. Fix ave/chunk can do that but can also time average those +values over many snapshots, or it can compute a temperature as if the +atoms in the chunk on different timesteps were collected together as +one set of atoms to calculate their temperature. This compute allows +the center-of-mass velocity of each chunk to be subtracted before +calculating the temperature; fix ave/chunk does not. -Note that only atoms in the specified group contribute to the -calculation. The "compute chunk/atom"_compute_chunk_atom.html command -defines its own group; atoms will have a chunk ID = 0 if they are not -in that group, signifying they are not assigned to a chunk, and will -thus also not contribute to this calculation. You can specify the -"all" group for this command if you simply want to include atoms with -non-zero chunk IDs. +IMPORTANT NOTE: Only atoms in the specified group contribute to the +calculations performed by this compute. The "compute +chunk/atom"_compute_chunk_atom.html command defines its own group; +atoms will have a chunk ID = 0 if they are not in that group, +signifying they are not assigned to a chunk, and will thus also not +contribute to this calculation. You can specify the "all" group for +this command if you simply want to include atoms with non-zero chunk +IDs. -The simplest way to output the pre-chunk results of the compute +The simplest way to output the per-chunk results of the compute temp/chunk calculation to a file is to use the "fix ave/time"_fix_ave_time.html command, for example: