Adding keywords for the thermo_style custom command (which can then be accessed by variables) was discussed diff --git a/doc/Section_modify.txt b/doc/Section_modify.txt index 5d84a71683..b56580024f 100644 --- a/doc/Section_modify.txt +++ b/doc/Section_modify.txt @@ -478,7 +478,7 @@ other variables = v_a, v_myvar, ... math functions = div(x,y), mult(x,y), add(x,y), ... group functions = mass(group), xcm(group,x), ... atom values = x[123], y[3], vx[34], ... -compute values = c_mytemp[0], c_thermo_pressure[3], ... +compute values = c_mytemp[0], c_thermo_press[3], ... Adding keywords for the "thermo_style custom"_themo_style.html command (which can then be accessed by variables) was discussed diff --git a/doc/Section_start.html b/doc/Section_start.html index 54c10b038d..17fd7a8984 100644 --- a/doc/Section_start.html +++ b/doc/Section_start.html @@ -186,15 +186,15 @@ the KSPACE package (see below).
(7) There are a few other -D compiler switches you can set as part of CCFLAGS. The read_data and dump commands will read/write gzipped -files if you compile with -DGZIP. It requires that your Unix support -the "popen" command. Using one of the -DPACK_ARRAY, -DPACK_POINTER, -and -DPACK_MEMCPY options can make for faster parallel FFTs (in the -PPPM solver) on some platforms. The -DPACK_ARRAY setting is the -default. If you compile with -DLAMMPS_XDR, the build will include XDR -compatability files for doing particle dumps in XTC format. This is -only necessary if your platform does have its own XDR files available. -See the Restrictions section of the dump command for -details. +files if you compile with -DLAMMPS_GZIP. It requires that your Unix +support the "popen" command. Using one of the -DPACK_ARRAY, +-DPACK_POINTER, and -DPACK_MEMCPY options can make for faster parallel +FFTs (in the PPPM solver) on some platforms. The -DPACK_ARRAY setting +is the default. If you compile with -DLAMMPS_XDR, the build will +include XDR compatability files for doing particle dumps in XTC +format. This is only necessary if your platform does have its own XDR +files available. See the Restrictions section of the dump +command for details.
(8) The DEPFLAGS setting is how the C++ compiler creates a dependency file for each source file. This speeds re-compilation when source diff --git a/doc/Section_start.txt b/doc/Section_start.txt index 7aaa0f8b9b..dbeab9469c 100644 --- a/doc/Section_start.txt +++ b/doc/Section_start.txt @@ -181,15 +181,15 @@ the KSPACE package (see below). (7) There are a few other -D compiler switches you can set as part of CCFLAGS. The read_data and dump commands will read/write gzipped -files if you compile with -DGZIP. It requires that your Unix support -the "popen" command. Using one of the -DPACK_ARRAY, -DPACK_POINTER, -and -DPACK_MEMCPY options can make for faster parallel FFTs (in the -PPPM solver) on some platforms. The -DPACK_ARRAY setting is the -default. If you compile with -DLAMMPS_XDR, the build will include XDR -compatability files for doing particle dumps in XTC format. This is -only necessary if your platform does have its own XDR files available. -See the Restrictions section of the "dump"_dump.html command for -details. +files if you compile with -DLAMMPS_GZIP. It requires that your Unix +support the "popen" command. Using one of the -DPACK_ARRAY, +-DPACK_POINTER, and -DPACK_MEMCPY options can make for faster parallel +FFTs (in the PPPM solver) on some platforms. The -DPACK_ARRAY setting +is the default. If you compile with -DLAMMPS_XDR, the build will +include XDR compatability files for doing particle dumps in XTC +format. This is only necessary if your platform does have its own XDR +files available. See the Restrictions section of the "dump"_dump.html +command for details. (8) The DEPFLAGS setting is how the C++ compiler creates a dependency file for each source file. This speeds re-compilation when source diff --git a/doc/compute.html b/doc/compute.html index 04d1957ab7..e35e9ea45e 100644 --- a/doc/compute.html +++ b/doc/compute.html @@ -76,11 +76,11 @@ computes for further info.
LAMMPS creates its own global computes for thermodynamic output. Three computes are always created, named "thermo_temp", -"thermo_pressure", and "thermo_pe", as if these commands had been -invoked in the input script: +"thermo_press", and "thermo_pe", as if these commands had been invoked +in the input script:
compute thermo_temp all temp -compute thermo_pressure all pressure thermo_temp +compute thermo_press all pressure thermo_temp compute thermo_pe all pe
Additional computes for other quantities are created if the thermo diff --git a/doc/compute.txt b/doc/compute.txt index 23411cd26a..d89bd9e928 100644 --- a/doc/compute.txt +++ b/doc/compute.txt @@ -73,11 +73,11 @@ computes for further info. LAMMPS creates its own global computes for thermodynamic output. Three computes are always created, named "thermo_temp", -"thermo_pressure", and "thermo_pe", as if these commands had been -invoked in the input script: +"thermo_press", and "thermo_pe", as if these commands had been invoked +in the input script: compute thermo_temp all temp -compute thermo_pressure all pressure thermo_temp +compute thermo_press all pressure thermo_temp compute thermo_pe all pe :pre Additional computes for other quantities are created if the thermo diff --git a/doc/compute_pressure.html b/doc/compute_pressure.html index 7db520ed72..686dddd52b 100644 --- a/doc/compute_pressure.html +++ b/doc/compute_pressure.html @@ -74,10 +74,10 @@ atoms or other degrees of freedom. where the DOF is specified by the temperature compute. See the various compute temperature styles for details.
-A compute of this style with the ID of "thermo_pressure" is created -when LAMMPS starts up, as if this command were in the input script: +
A compute of this style with the ID of "thermo_press" is created when +LAMMPS starts up, as if this command were in the input script:
-compute thermo_pressure all pressure thermo_temp +compute thermo_press all pressure thermo_tempwhere "thermo_temp" is the ID of a similarly defined compute of style "temp". See the "thermo_style" command for more details. diff --git a/doc/compute_pressure.txt b/doc/compute_pressure.txt index 2f7c4f2977..0a26fc4f60 100644 --- a/doc/compute_pressure.txt +++ b/doc/compute_pressure.txt @@ -71,10 +71,10 @@ Note that the N is the above formula is really degrees-of-freedom where the DOF is specified by the temperature compute. See the various "compute temperature"_compute.html styles for details. -A compute of this style with the ID of "thermo_pressure" is created -when LAMMPS starts up, as if this command were in the input script: +A compute of this style with the ID of "thermo_press" is created when +LAMMPS starts up, as if this command were in the input script: -compute thermo_pressure all pressure thermo_temp :pre +compute thermo_press all pressure thermo_temp :pre where "thermo_temp" is the ID of a similarly defined compute of style "temp". See the "thermo_style" command for more details. diff --git a/doc/dump.html b/doc/dump.html index f797a39bb1..2ebf962971 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -309,9 +309,9 @@ used to change it. The exception is DCD files which store the tilt factors for subsequent visualization by programs like VMD.
-To write gzipped dump files, you must compile LAMMPS with the -DGZIP -option - see the Making LAMMPS section of the -documentation. +
To write gzipped dump files, you must compile LAMMPS with the +-DLAMMPS_GZIP option - see the Making LAMMPS +section of the documentation.
The bond style is part of the "molecular" package. It is only enabled if LAMMPS was built with that package. See the Making diff --git a/doc/dump.txt b/doc/dump.txt index 57491d7462..0234c62526 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -299,9 +299,9 @@ used to change it. The exception is DCD files which store the tilt factors for subsequent visualization by programs like "VMD"_http://www.ks.uiuc.edu/Research/vmd. -To write gzipped dump files, you must compile LAMMPS with the -DGZIP -option - see the "Making LAMMPS"_Section_start.html#2_2 section of the -documentation. +To write gzipped dump files, you must compile LAMMPS with the +-DLAMMPS_GZIP option - see the "Making LAMMPS"_Section_start.html#2_2 +section of the documentation. The {bond} style is part of the "molecular" package. It is only enabled if LAMMPS was built with that package. See the "Making diff --git a/doc/fix_ave_time.html b/doc/fix_ave_time.html index 7f34c8ed22..a25bcd281f 100644 --- a/doc/fix_ave_time.html +++ b/doc/fix_ave_time.html @@ -51,7 +51,7 @@
Examples:
fix 1 all ave/time 100 5 1000 myTemp thermo_temp file temp.profile -fix 1 all ave/time 100 5 1000 thermo_pressure2 ave window 20 +fix 1 all ave/time 100 5 1000 thermo_press2 ave window 20 fix 1 all ave/time 1 100 1000 f_indent f_indent1 file temp.indentDescription: diff --git a/doc/fix_ave_time.txt b/doc/fix_ave_time.txt index 28ac9a3304..d1abac324c 100644 --- a/doc/fix_ave_time.txt +++ b/doc/fix_ave_time.txt @@ -38,7 +38,7 @@ keyword = {file} or {ave} :l [Examples:] fix 1 all ave/time 100 5 1000 myTemp thermo_temp file temp.profile -fix 1 all ave/time 100 5 1000 thermo_pressure[2] ave window 20 +fix 1 all ave/time 100 5 1000 thermo_press[2] ave window 20 fix 1 all ave/time 1 100 1000 f_indent f_indent[1] file temp.indent :pre [Description:] diff --git a/doc/fix_nph.html b/doc/fix_nph.html index 4553324532..9e2b3354ae 100644 --- a/doc/fix_nph.html +++ b/doc/fix_nph.html @@ -139,13 +139,13 @@ as the fix group.
Note that these are NOT the computes used by thermodynamic output (see the thermo_style command) with ID = thermo_temp -and thermo_pressure. This means you can change the attributes of -this fix's temperature or pressure via the +and thermo_press. This means you can change the attributes of this +fix's temperature or pressure via the compute_modify command or print this temperature or pressure during thermodyanmic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp or -thermo_pressure will have no effect on this fix. +thermo_press will have no effect on this fix.
Restart, fix_modify, output, run start/stop, minimize info:
diff --git a/doc/fix_nph.txt b/doc/fix_nph.txt index 06359cfbc2..0acd1c2c79 100644 --- a/doc/fix_nph.txt +++ b/doc/fix_nph.txt @@ -129,13 +129,13 @@ as the fix group. Note that these are NOT the computes used by thermodynamic output (see the "thermo_style"_thermo_style.html command) with ID = {thermo_temp} -and {thermo_pressure}. This means you can change the attributes of -this fix's temperature or pressure via the +and {thermo_press}. This means you can change the attributes of this +fix's temperature or pressure via the "compute_modify"_compute_modify.html command or print this temperature or pressure during thermodyanmic output via the "thermo_style custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} or -{thermo_pressure} will have no effect on this fix. +{thermo_press} will have no effect on this fix. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/fix_npt.html b/doc/fix_npt.html index cc4eaa631f..355f98575e 100644 --- a/doc/fix_npt.html +++ b/doc/fix_npt.html @@ -143,13 +143,13 @@ as the fix group.Note that these are NOT the computes used by thermodynamic output (see the thermo_style command) with ID = thermo_temp -and thermo_pressure. This means you can change the attributes of -this fix's temperature or pressure via the +and thermo_press. This means you can change the attributes of this +fix's temperature or pressure via the compute_modify command or print this temperature or pressure during thermodyanmic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp or -thermo_pressure will have no effect on this fix. +thermo_press will have no effect on this fix.
Restart, fix_modify, output, run start/stop, minimize info:
diff --git a/doc/fix_npt.txt b/doc/fix_npt.txt index 72d95f6045..77d9cff9ae 100644 --- a/doc/fix_npt.txt +++ b/doc/fix_npt.txt @@ -132,13 +132,13 @@ as the fix group. Note that these are NOT the computes used by thermodynamic output (see the "thermo_style"_thermo_style.html command) with ID = {thermo_temp} -and {thermo_pressure}. This means you can change the attributes of -this fix's temperature or pressure via the +and {thermo_press}. This means you can change the attributes of this +fix's temperature or pressure via the "compute_modify"_compute_modify.html command or print this temperature or pressure during thermodyanmic output via the "thermo_style custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} or -{thermo_pressure} will have no effect on this fix. +{thermo_press} will have no effect on this fix. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/fix_npt_asphere.html b/doc/fix_npt_asphere.html index dd24f725b6..56da54ee97 100644 --- a/doc/fix_npt_asphere.html +++ b/doc/fix_npt_asphere.html @@ -142,13 +142,13 @@ as the fix group.Note that these are NOT the computes used by thermodynamic output (see the thermo_style command) with ID = thermo_temp -and thermo_pressure. This means you can change the attributes of -this fix's temperature or pressure via the +and thermo_press. This means you can change the attributes of this +fix's temperature or pressure via the compute_modify command or print this temperature or pressure during thermodyanmic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp or -thermo_pressure will have no effect on this fix. +thermo_press will have no effect on this fix.
Restart, fix_modify, output, run start/stop, minimize info:
diff --git a/doc/fix_npt_asphere.txt b/doc/fix_npt_asphere.txt index 1e8004ee94..484cd2a49a 100755 --- a/doc/fix_npt_asphere.txt +++ b/doc/fix_npt_asphere.txt @@ -131,13 +131,13 @@ as the fix group. Note that these are NOT the computes used by thermodynamic output (see the "thermo_style"_thermo_style.html command) with ID = {thermo_temp} -and {thermo_pressure}. This means you can change the attributes of -this fix's temperature or pressure via the +and {thermo_press}. This means you can change the attributes of this +fix's temperature or pressure via the "compute_modify"_compute_modify.html command or print this temperature or pressure during thermodyanmic output via the "thermo_style custom"_thermo_style.html command using the appropriate compute-ID. It also means that changing attributes of {thermo_temp} or -{thermo_pressure} will have no effect on this fix. +{thermo_press} will have no effect on this fix. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/fix_tmd.html b/doc/fix_tmd.html index f2aa769e97..68609efac3 100644 --- a/doc/fix_tmd.html +++ b/doc/fix_tmd.html @@ -41,7 +41,8 @@ group and the target coordinates listed in file1. Thus a value of rho_final = 0.0 means move the atoms all the way to the final structure during the course of the run. -The format of the target file1 is as follows: +
The target file1 can be ASCII text or a gzipped text file (detected by +a .gz suffix). The format of the target file1 is as follows:
0.0 25.0 xlo xhi 0.0 25.0 ylo yhi @@ -112,6 +113,10 @@ which a SHAKE fix is applied. This is because LAMMPS assumes there are not multiple competing holonomic constraints applied to the same atoms. +To read gzipped target files, you must compile LAMMPS with the +-DLAMMPS_GZIP option - see the Making LAMMPS +section of the documentation. +
Related commands: none
Default: none diff --git a/doc/fix_tmd.txt b/doc/fix_tmd.txt index 3530b4f4e6..a522a31441 100644 --- a/doc/fix_tmd.txt +++ b/doc/fix_tmd.txt @@ -38,7 +38,8 @@ group and the target coordinates listed in file1. Thus a value of rho_final = 0.0 means move the atoms all the way to the final structure during the course of the run. -The format of the target file1 is as follows: +The target file1 can be ASCII text or a gzipped text file (detected by +a .gz suffix). The format of the target file1 is as follows: 0.0 25.0 xlo xhi 0.0 25.0 ylo yhi @@ -109,6 +110,10 @@ which a SHAKE fix is applied. This is because LAMMPS assumes there are not multiple competing holonomic constraints applied to the same atoms. +To read gzipped target files, you must compile LAMMPS with the +-DLAMMPS_GZIP option - see the "Making LAMMPS"_Section_start.html#2_2 +section of the documentation. + [Related commands:] none [Default:] none diff --git a/doc/read_data.html b/doc/read_data.html index 7efc64cc61..9491d9559a 100644 --- a/doc/read_data.html +++ b/doc/read_data.html @@ -684,9 +684,9 @@ units of angular velocity (radians/time).
Restrictions:
-To read gzipped data files, you must compile LAMMPS with the -DGZIP -option - see the Making LAMMPS section of the -documentation. +
To read gzipped data files, you must compile LAMMPS with the +-DLAMMPS_GZIP option - see the Making LAMMPS +section of the documentation.
Related commands:
diff --git a/doc/read_data.txt b/doc/read_data.txt index 486d6eaa5f..1ba88d7fe9 100644 --- a/doc/read_data.txt +++ b/doc/read_data.txt @@ -594,9 +594,9 @@ Translational velocities can also be set by the [Restrictions:] -To read gzipped data files, you must compile LAMMPS with the -DGZIP -option - see the "Making LAMMPS"_Section_start.html#2_2 section of the -documentation. +To read gzipped data files, you must compile LAMMPS with the +-DLAMMPS_GZIP option - see the "Making LAMMPS"_Section_start.html#2_2 +section of the documentation. [Related commands:] diff --git a/doc/thermo_modify.html b/doc/thermo_modify.html index 35d7991b6b..2b9aecebcb 100644 --- a/doc/thermo_modify.html +++ b/doc/thermo_modify.html @@ -99,8 +99,8 @@ compute ID must have been previously defined by the user via the compute command and it must be a style of compute that calculates a pressure. As described in the thermo_style command, thermo output uses a default -compute for pressure with ID = thermo_pressure. This option allows -the user to override the default. +compute for pressure with ID = thermo_press. This option allows the +user to override the default.The drot keyword is used to determine how rotational energy is calculated for dipolar atoms, which is used by the thermo_style diff --git a/doc/thermo_modify.txt b/doc/thermo_modify.txt index 7085416ebe..2cff6219bf 100644 --- a/doc/thermo_modify.txt +++ b/doc/thermo_modify.txt @@ -93,8 +93,8 @@ compute ID must have been previously defined by the user via the "compute"_compute.html command and it must be a style of compute that calculates a pressure. As described in the "thermo_style"_thermo_style.html command, thermo output uses a default -compute for pressure with ID = {thermo_pressure}. This option allows -the user to override the default. +compute for pressure with ID = {thermo_press}. This option allows the +user to override the default. The {drot} keyword is used to determine how rotational energy is calculated for dipolar atoms, which is used by the thermo_style diff --git a/doc/thermo_style.html b/doc/thermo_style.html index 56d5ac5668..95c96cf25c 100644 --- a/doc/thermo_style.html +++ b/doc/thermo_style.html @@ -139,13 +139,13 @@ This is done via the thermo_modify command.
Several of the thermodynamic quantities require a pressure to be computed: "press", "enthalpy", "pxx", etc. By default this is done by -using the "thermo_pressure" compute which is created when LAMMPS -starts up, as if this command had been issued: +using the pressure compute which is created when LAMMPS starts up, as +if this command had been issued:
-compute thermo_pressure all pressure thermo_temp +compute thermo_press all pressure thermo_tempSee the compute pressure command for details. -Note that the ID of this compute is thermo_pressure and the group is +Note that the ID of this compute is thermo_press and the group is all. You can change the attributes of this pressure via the compute_modify command. Alternatively, you can directly assign a new compute (that calculates pressure) which you diff --git a/doc/thermo_style.txt b/doc/thermo_style.txt index df2177c0c9..cb31377177 100644 --- a/doc/thermo_style.txt +++ b/doc/thermo_style.txt @@ -133,13 +133,13 @@ This is done via the "thermo_modify"_thermo_modify.html command. Several of the thermodynamic quantities require a pressure to be computed: "press", "enthalpy", "pxx", etc. By default this is done by -using the "thermo_pressure" compute which is created when LAMMPS -starts up, as if this command had been issued: +using the pressure compute which is created when LAMMPS starts up, as +if this command had been issued: -compute thermo_pressure all pressure thermo_temp :pre +compute thermo_press all pressure thermo_temp :pre See the "compute pressure"_compute_pressure.html command for details. -Note that the ID of this compute is {thermo_pressure} and the group is +Note that the ID of this compute is {thermo_press} and the group is {all}. You can change the attributes of this pressure via the "compute_modify"_compute_modify.html command. Alternatively, you can directly assign a new compute (that calculates pressure) which you