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Merge pull request #1853 from akohlmey/collected-small-changes

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Collected small changes and bugfixes for the next patch release
This commit is contained in:
Axel Kohlmeyer
2020-01-22 17:25:03 -05:00
committed by GitHub
parent 8096a78340 61ddf9bcd8
commit 30444b344b
22 changed files with 69 additions and 1526 deletions
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3
doc/src/Errors_messages.rst
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@ -489,6 +489,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
Only systems with bonds that can be changed can be used. Atom\_style
template does not qualify.
*Bond/react: Invalid template atom ID in map file*
Atom IDs in molecule templates range from 1 to the number of atoms in the template.
*Bond/react: Rmax cutoff is longer than pairwise cutoff*
This is not allowed because bond creation is done using the pairwise
neighbor list.

4
doc/src/Howto_bash.rst
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@ -115,8 +115,8 @@ Files in Ubuntu on Windows
^^^^^^^^^^^^^^^^^^^^^^^^^^
When you launch "Bash on Ubuntu on Windows" you will start out in your Linux
user home directory /home/\ **username**\ . You can access your Windows user directory
using the /mnt/c/Users/\ **username** folder.
user home directory /home/[username]\ . You can access your Windows user directory
using the /mnt/c/Users/[username] folder.
Download LAMMPS
^^^^^^^^^^^^^^^

8
doc/src/compute_angle_local.rst
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@ -81,12 +81,12 @@ and output the statistics in various ways:
compute 1 all property/local aatom1 aatom2 aatom3 atype
compute 2 all angle/local eng theta v_cos v_cossq set theta t
dump 1 all local 100 tmp.dump c_1**\*** c_2**\***
dump 1 all local 100 tmp.dump c_1[*] c_2[*]
compute 3 all reduce ave c_2**\***
thermo_style custom step temp press c_3**\***
compute 3 all reduce ave c_2[*]
thermo_style custom step temp press c_3[*]
fix 10 all ave/histo 10 10 100 -1 1 20 c_2\ **3** mode vector file tmp.histo
fix 10 all ave/histo 10 10 100 -1 1 20 c_2[3] mode vector file tmp.histo
The :doc:`dump local <dump>` command will output the energy, angle,
cosine(angle), cosine\^2(angle) for every angle in the system. The

8
doc/src/compute_bond_local.rst
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@ -134,12 +134,12 @@ output the statistics in various ways:
compute 1 all property/local batom1 batom2 btype
compute 2 all bond/local engpot dist v_dsq set dist d
dump 1 all local 100 tmp.dump c_1**\*** c_2**\***
dump 1 all local 100 tmp.dump c_1[*] c_2[*]
compute 3 all reduce ave c_2**\***
thermo_style custom step temp press c_3**\***
compute 3 all reduce ave c_2[*]
thermo_style custom step temp press c_3[*]
fix 10 all ave/histo 10 10 100 0 6 20 c_2\ **3** mode vector file tmp.histo
fix 10 all ave/histo 10 10 100 0 6 20 c_2[3] mode vector file tmp.histo
The :doc:`dump local <dump>` command will output the energy, distance,
distance\^2 for every bond in the system. The

8
doc/src/compute_chunk_spread_atom.rst
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@ -32,7 +32,7 @@ Examples
.. parsed-literal::
compute 1 all chunk/spread/atom mychunk c_com**\*** c_gyration
compute 1 all chunk/spread/atom mychunk c_com[*] c_gyration
Description
"""""""""""
@ -109,7 +109,7 @@ with 3 columns:
.. parsed-literal::
compute com all com/chunk mychunk
compute 10 all chunk/spread/atom mychunk c_com[\*]
compute 10 all chunk/spread/atom mychunk c_com[*]
compute 10 all chunk/spread/atom mychunk c_com[1] c_com[2] c_com[3]
@ -125,8 +125,8 @@ to the bench/in.chain script.
compute cmol all chunk/atom molecule
compute com all com/chunk cmol
compute comchunk all chunk/spread/atom cmol c_com**\***
dump 1 all custom 50 tmp.dump id mol type x y z c_comchunk**\***
compute comchunk all chunk/spread/atom cmol c_com[*]
dump 1 all custom 50 tmp.dump id mol type x y z c_comchunk[*]
dump_modify 1 sort id
The same per-chunk data for each atom could be used to define per-atom

8
doc/src/compute_dihedral_local.rst
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@ -79,12 +79,12 @@ the system and output the statistics in various ways:
compute 1 all property/local datom1 datom2 datom3 datom4 dtype
compute 2 all dihedral/local phi v_cos v_cossq set phi p
dump 1 all local 100 tmp.dump c_1**\*** c_2**\***
dump 1 all local 100 tmp.dump c_1[*] c_2[*]
compute 3 all reduce ave c_2**\***
thermo_style custom step temp press c_3**\***
compute 3 all reduce ave c_2[*]
thermo_style custom step temp press c_3[*]
fix 10 all ave/histo 10 10 100 -1 1 20 c_2\ **2** mode vector file tmp.histo
fix 10 all ave/histo 10 10 100 -1 1 20 c_2[2] mode vector file tmp.histo
The :doc:`dump local <dump>` command will output the angle,
cosine(angle), cosine\^2(angle) for every dihedral in the system. The

4
doc/src/compute_displace_atom.rst
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@ -94,10 +94,10 @@ something like the following commands:
write_dump all custom tmp.dump id type x y z # see comment below
variable Dhop equal 0.6
variable check atom "c_dsp\ **4** > v_Dhop"
variable check atom "c_dsp[4] > v_Dhop"
compute dsp all displace/atom refresh check
dump 1 all custom 100 tmp.dump id type x y z
dump_modify 1 append yes thresh c_dsp\ **4** > $\ *Dhop* &
dump_modify 1 append yes thresh c_dsp[4] > ${Dhop} &
refresh c_dsp delay 100
The :doc:`dump\_modify thresh <dump_modify>` command will only output

2
doc/src/fix_ave_chunk.rst
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@ -440,7 +440,7 @@ By default, these header lines are as follows:
In the first line, ID and name are replaced with the fix-ID and group
name. The second line describes the two values that are printed at
the first of each section of output. In the third line the values are
replaced with the appropriate value names, e.g. fx or c\_myCompute\ **2**\ .
replaced with the appropriate value names, e.g. fx or c\_myCompute[2].
The words in parenthesis only appear with corresponding columns if the
chunk style specified for the :doc:`compute chunk/atom <compute_chunk_atom>` command supports them. The OrigID

204
doc/txt/Howto_bash.txt
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@ -1,204 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
Using LAMMPS with Bash on Windows :h3
[written by Richard Berger]
:line
Starting with Windows 10 you can install Linux tools directly in Windows. This
allows you to compile LAMMPS following the same procedure as on a real Ubuntu
Linux installation. Software can be easily installed using the package manager
via apt-get and all files are accessible in both the Windows Explorer and your
Linux shell (bash). This avoids switching to a different operating system or
installing a virtual machine. Everything runs on Windows.
Installing Bash on Windows :h4
Prerequisites :h5
Windows 10 (64bit only)
Latest updates installed :ul
Enable developer mode :h5
You enable this feature by first opening Windows Settings and enabling
Developer mode. Go to the Windows settings and search for "developer". This
will allow you to install software which comes from outside of the Windows
Store. You might be prompted to reboot your compute. Please do so.
:image(JPG/bow_tutorial_01_small.png,JPG/bow_tutorial_01.png)
:image(JPG/bow_tutorial_02_small.png,JPG/bow_tutorial_02.png)
:image(JPG/bow_tutorial_03_small.png,JPG/bow_tutorial_03.png)
Install Windows Subsystem for Linux :h5
Next you must ensure that the Window Subsystem for Linux is installed. Again,
search for "enable windows features" in the Settings dialog. This opens a
dialog with a list of features you can install. Add a checkmark to Windows
Subsystem for Linux (Beta) and press OK.
:image(JPG/bow_tutorial_04_small.png,JPG/bow_tutorial_04.png)
:image(JPG/bow_tutorial_05.png,JPG/bow_tutorial_05.png)
Install Bash for Windows :h5
After installation completes, type "bash" in the Windows Start menu search.
Select the first found option. This will launch a command-line window which
will prompt you about installing Ubuntu on Windows. Confirm with "y" and press
enter. This will then download Ubuntu for Windows.
:image(JPG/bow_tutorial_06.png)
:image(JPG/bow_tutorial_07.png)
During installation, you will be asked for a new password. This will be used
for installing new software and running commands with sudo.
:image(JPG/bow_tutorial_08.png)
Type exit to close the command-line window.
Go to the Start menu and type "bash" again. This time you will see a "Bash on
Ubuntu on Windows" Icon. Start this program.
:image(JPG/bow_tutorial_09.png)
Congratulations, you have installed [Bash on Ubuntu on Windows].
:image(JPG/bow_tutorial_10.png)
:line
Compiling LAMMPS in Bash on Windows :h4
The installation of LAMMPS in this environment is identical to working inside
of a real Ubuntu Linux installation. At the time writing, it uses Ubuntu 16.04.
Installing prerequisite packages :h5
First upgrade all existing packages using
sudo apt update
sudo apt upgrade -y :pre
Next install the following packages, which include compilers and libraries
needed for various LAMMPS features:
sudo apt install -y build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng12-dev python-dev python-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tools :pre
Files in Ubuntu on Windows :h5
When you launch "Bash on Ubuntu on Windows" you will start out in your Linux
user home directory /home/[username]. You can access your Windows user directory
using the /mnt/c/Users/[username] folder.
Download LAMMPS :h5
Obtain a copy of the LAMMPS code and go into it using "cd"
Option 1: Downloading LAMMPS tarball using wget :h6
wget http://lammps.sandia.gov/tars/lammps-stable.tar.gz
tar xvzf lammps-stable.tar.gz
cd lammps-31Mar17 :pre
Option 2: Obtaining LAMMPS code from GitHub :h6
git clone https://github.com/lammps/lammps.git
cd lammps :pre
Compiling LAMMPS :h5
At this point you can compile LAMMPS like on Ubuntu Linux.
Compiling serial version :h6
cd src/
make -j 4 serial :pre
This will create an executable called lmp_serial in the src/ directory
Compiling MPI version :h6
cd src/
make -j 4 mpi :pre
This will create an executable called lmp_mpi in the src/ directory
:line
Finally, please note the absolute path of your src folder. You can get this using
pwd :pre
or
echo $PWD :pre
To run any examples you need the location of the executable. For now, let us
save this location in a temporary variable
LAMMPS_DIR=$PWD :pre
:line
Running an example script :h5
Once compiled you can execute some of the LAMMPS examples. Switch into the
examples/melt folder
cd ../examples/melt :pre
The full path of the serial executable is $LAMMPS_DIR/lmp_serial, while the mpi
version is $LAMMPS_DIR/lmp_mpi. You can run the melt example with either
version as follows:
$LAMMPS_DIR/lmp_serial -in in.melt :pre
or
mpirun -np 4 $LAMMPS_DIR/lmp_mpi -in in.melt :pre
Note the use of our variable $LAMMPS_DIR, which expands into the full path of
the LAMMPS src folder we saved earlier.
Adding your executable directory to your PATH :h6
You can avoid having to type the full path of your LAMMPS binary by adding its
parent folder to the PATH environment variable as follows:
export PATH=$LAMMPS_DIR:$PATH :pre
Input scripts can then be run like this:
lmp_serial -in in.melt :pre
or
mpirun -np 4 lmp_mpi -in in.melt :pre
However, this PATH variable will not persist if you close your bash window.
To persist this setting edit the $HOME/.bashrc file using your favorite editor
and add this line
export PATH=/full/path/to/your/lammps/src:$PATH :pre
[Example:]
For an executable lmp_serial with a full path
/home/richard/lammps/src/lmp_serial :pre
the PATH variable should be
export PATH=/home/richard/lammps/src:$PATH :pre
NOTE: This should give you a jump start when trying to run LAMMPS on Windows.
To become effective in this environment I encourage you to look into Linux
tutorials explaining Bash and Basic Unix commands (e.g., "Linux
Journey"_https://linuxjourney.com)

135
doc/txt/compute_angle_local.txt
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@ -1,135 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
compute angle/local command :h3
[Syntax:]
compute ID group-ID angle/local value1 value2 ... keyword args ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
angle/local = style name of this compute command :l
one or more values may be appended :l
value = {theta} or {eng} or {v_name} :l
{theta} = tabulate angles
{eng} = tabulate angle energies
{v_name} = equal-style variable with name (see below) :pre
zero or more keyword/args pairs may be appended :l
keyword = {set} :l
{set} args = theta name
theta = only currently allowed arg
name = name of variable to set with theta :pre
:ule
[Examples:]
compute 1 all angle/local theta
compute 1 all angle/local eng theta
compute 1 all angle/local theta v_cos set theta t :pre
[Description:]
Define a computation that calculates properties of individual angle
interactions. The number of datums generated, aggregated across all
processors, equals the number of angles in the system, modified by the
group parameter as explained below.
The value {theta} is the angle for the 3 atoms in the interaction.
The value {eng} is the interaction energy for the angle.
The value {v_name} can be used together with the {set} keyword to
compute a user-specified function of the angle theta. The {name}
specified for the {v_name} value is the name of an "equal-style
variable"_variable.html which should evaluate a formula based on a
variable which will store the angle theta. This other variable must
be an "internal-style variable"_variable.html defined in the input
script; its initial numeric value can be anything. It must be an
internal-style variable, because this command resets its value
directly. The {set} keyword is used to identify the name of this
other variable associated with theta.
Note that the value of theta for each angle which stored in the
internal variable is in radians, not degrees.
As an example, these commands can be added to the bench/in.rhodo
script to compute the cosine and cosine^2 of every angle in the system
and output the statistics in various ways:
variable t internal 0.0
variable cos equal cos(v_t)
variable cossq equal cos(v_t)*cos(v_t) :pre
compute 1 all property/local aatom1 aatom2 aatom3 atype
compute 2 all angle/local eng theta v_cos v_cossq set theta t
dump 1 all local 100 tmp.dump c_1[*] c_2[*] :pre
compute 3 all reduce ave c_2[*]
thermo_style custom step temp press c_3[*] :pre
fix 10 all ave/histo 10 10 100 -1 1 20 c_2[3] mode vector file tmp.histo :pre
The "dump local"_dump.html command will output the energy, angle,
cosine(angle), cosine^2(angle) for every angle in the system. The
"thermo_style"_thermo_style.html command will print the average of
those quantities via the "compute reduce"_compute_reduce.html command
with thermo output. And the "fix ave/histo"_fix_ave_histo.html
command will histogram the cosine(angle) values and write them to a
file.
:line
The local data stored by this command is generated by looping over all
the atoms owned on a processor and their angles. An angle will only
be included if all 3 atoms in the angle are in the specified compute
group. Any angles that have been broken (see the
"angle_style"_angle_style.html command) by setting their angle type to
0 are not included. Angles that have been turned off (see the "fix
shake"_fix_shake.html or "delete_bonds"_delete_bonds.html commands) by
setting their angle type negative are written into the file, but their
energy will be 0.0.
Note that as atoms migrate from processor to processor, there will be
no consistent ordering of the entries within the local vector or array
from one timestep to the next. The only consistency that is
guaranteed is that the ordering on a particular timestep will be the
same for local vectors or arrays generated by other compute commands.
For example, angle output from the "compute
property/local"_compute_property_local.html command can be combined
with data from this command and output by the "dump local"_dump.html
command in a consistent way.
Here is an example of how to do this:
compute 1 all property/local atype aatom1 aatom2 aatom3
compute 2 all angle/local theta eng
dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_1\[4\] c_2\[1\] c_2\[2\] :pre
[Output info:]
This compute calculates a local vector or local array depending on the
number of values. The length of the vector or number of rows in the
array is the number of angles. If a single value is specified, a
local vector is produced. If two or more values are specified, a
local array is produced where the number of columns = the number of
values. The vector or array can be accessed by any command that uses
local values from a compute as input. See the "Howto
output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The output for {theta} will be in degrees. The output for {eng} will
be in energy "units"_units.html.
[Restrictions:] none
[Related commands:]
"dump local"_dump.html, "compute
property/local"_compute_property_local.html
[Default:] none

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doc/txt/compute_bond_local.txt
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@ -1,187 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
compute bond/local command :h3
[Syntax:]
compute ID group-ID bond/local value1 value2 ... keyword args ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
bond/local = style name of this compute command :l
one or more values may be appended :l
value = {dist} or {engpot} or {force} or {fx} or {fy} or {fz} or {engvib} or {engrot} or {engtrans} or {omega} or {velvib} or {v_name} :l
{dist} = bond distance
{engpot} = bond potential energy
{force} = bond force :pre
{fx},{fy},{fz} = components of bond force
{engvib} = bond kinetic energy of vibration
{engrot} = bond kinetic energy of rotation
{engtrans} = bond kinetic energy of translation
{omega} = magnitude of bond angular velocity
{velvib} = vibrational velocity along the bond length
{v_name} = equal-style variable with name (see below) :pre
zero or more keyword/args pairs may be appended :l
keyword = {set} :l
{set} args = dist name
dist = only currently allowed arg
name = name of variable to set with distance (dist) :pre
:ule
:ule
[Examples:]
compute 1 all bond/local engpot
compute 1 all bond/local dist engpot force :pre
compute 1 all bond/local dist fx fy fz :pre
compute 1 all angle/local dist v_distsq set dist d :pre
[Description:]
Define a computation that calculates properties of individual bond
interactions. The number of datums generated, aggregated across all
processors, equals the number of bonds in the system, modified by the
group parameter as explained below.
All these properties are computed for the pair of atoms in a bond,
whether the 2 atoms represent a simple diatomic molecule, or are part
of some larger molecule.
The value {dist} is the current length of the bond.
The value {engpot} is the potential energy for the bond,
based on the current separation of the pair of atoms in the bond.
The value {force} is the magnitude of the force acting between the
pair of atoms in the bond.
The values {fx}, {fy}, and {fz} are the xyz components of
{force} between the pair of atoms in the bond.
The remaining properties are all computed for motion of the two atoms
relative to the center of mass (COM) velocity of the 2 atoms in the
bond.
The value {engvib} is the vibrational kinetic energy of the two atoms
in the bond, which is simply 1/2 m1 v1^2 + 1/2 m2 v2^2, where v1 and
v2 are the magnitude of the velocity of the 2 atoms along the bond
direction, after the COM velocity has been subtracted from each.
The value {engrot} is the rotational kinetic energy of the two atoms
in the bond, which is simply 1/2 m1 v1^2 + 1/2 m2 v2^2, where v1 and
v2 are the magnitude of the velocity of the 2 atoms perpendicular to
the bond direction, after the COM velocity has been subtracted from
each.
The value {engtrans} is the translational kinetic energy associated
with the motion of the COM of the system itself, namely 1/2 (m1+m2)
Vcm^2 where Vcm = magnitude of the velocity of the COM.
Note that these 3 kinetic energy terms are simply a partitioning of
the summed kinetic energy of the 2 atoms themselves. I.e. total KE =
1/2 m1 v1^2 + 1/2 m2 v2^2 = engvib + engrot + engtrans, where v1,v2
are the magnitude of the velocities of the 2 atoms, without any
adjustment for the COM velocity.
The value {omega} is the magnitude of the angular velocity of the
two atoms around their COM position.
The value {velvib} is the magnitude of the relative velocity of the
two atoms in the bond towards each other. A negative value means the
2 atoms are moving toward each other; a positive value means they are
moving apart.
The value {v_name} can be used together with the {set} keyword to
compute a user-specified function of the bond distance. The {name}
specified for the {v_name} value is the name of an "equal-style
variable"_variable.html which should evaluate a formula based on a
variable which will store the bond distance. This other variable must
be an "internal-style variable"_variable.html defined in the input
script; its initial numeric value can be anything. It must be an
internal-style variable, because this command resets its value
directly. The {set} keyword is used to identify the name of this
other variable associated with theta.
As an example, these commands can be added to the bench/in.rhodo
script to compute the distance^2 of every bond in the system and
output the statistics in various ways:
variable d internal 0.0
variable dsq equal v_d*v_d :pre
compute 1 all property/local batom1 batom2 btype
compute 2 all bond/local engpot dist v_dsq set dist d
dump 1 all local 100 tmp.dump c_1[*] c_2[*] :pre
compute 3 all reduce ave c_2[*]
thermo_style custom step temp press c_3[*] :pre
fix 10 all ave/histo 10 10 100 0 6 20 c_2[3] mode vector file tmp.histo :pre
The "dump local"_dump.html command will output the energy, distance,
distance^2 for every bond in the system. The
"thermo_style"_thermo_style.html command will print the average of
those quantities via the "compute reduce"_compute_reduce.html command
with thermo output. And the "fix ave/histo"_fix_ave_histo.html
command will histogram the distance^2 values and write them to a file.
:line
The local data stored by this command is generated by looping over all
the atoms owned on a processor and their bonds. A bond will only be
included if both atoms in the bond are in the specified compute group.
Any bonds that have been broken (see the "bond_style"_bond_style.html
command) by setting their bond type to 0 are not included. Bonds that
have been turned off (see the "fix shake"_fix_shake.html or
"delete_bonds"_delete_bonds.html commands) by setting their bond type
negative are written into the file, but their energy will be 0.0.
Note that as atoms migrate from processor to processor, there will be
no consistent ordering of the entries within the local vector or array
from one timestep to the next. The only consistency that is
guaranteed is that the ordering on a particular timestep will be the
same for local vectors or arrays generated by other compute commands.
For example, bond output from the "compute
property/local"_compute_property_local.html command can be combined
with data from this command and output by the "dump local"_dump.html
command in a consistent way.
Here is an example of how to do this:
compute 1 all property/local btype batom1 batom2
compute 2 all bond/local dist engpot
dump 1 all local 1000 tmp.dump index c_1\[*\] c_2\[*\] :pre
[Output info:]
This compute calculates a local vector or local array depending on the
number of values. The length of the vector or number of rows in the
array is the number of bonds. If a single value is specified, a local
vector is produced. If two or more values are specified, a local
array is produced where the number of columns = the number of values.
The vector or array can be accessed by any command that uses local
values from a compute as input. See the "Howto
output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The output for {dist} will be in distance "units"_units.html. The
output for {velvib} will be in velocity "units"_units.html. The output
for {omega} will be in velocity/distance "units"_units.html. The
output for {engtrans}, {engvib}, {engrot}, and {engpot} will be in
energy "units"_units.html. The output for {force} will be in force
"units"_units.html.
[Restrictions:] none
[Related commands:]
"dump local"_dump.html, "compute
property/local"_compute_property_local.html
[Default:] none

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doc/txt/compute_chunk_spread_atom.txt
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@ -1,203 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
compute chunk/spread/atom command :h3
[Syntax:]
compute ID group-ID chunk/spread/atom chunkID input1 input2 ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
chunk/spread/atom = style name of this compute command :l
chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l
one or more inputs can be listed :l
input = c_ID, c_ID\[N\], f_ID, f_ID\[N\] :l
c_ID = global vector calculated by a compute with ID
c_ID\[I\] = Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
f_ID = global vector calculated by a fix with ID
f_ID\[I\] = Ith column of global array calculated by a fix with ID, I can include wildcard (see below) :pre
:ule
[Examples:]
compute 1 all chunk/spread/atom mychunk c_com[*] c_gyration :pre
[Description:]
Define a calculation that "spreads" one or more per-chunk values to
each atom in the chunk. This can be useful in several scenarios:
For creating a "dump file"_dump.html where each atom lists info about
the chunk it is in, e.g. for post-processing purposes. :ulb,l
To access chunk value in "atom-style variables"_variable.html that
need info about the chunk each atom is in. :l
To use the "fix ave/chunk"_fix_ave_chunk.html command to spatially
average per-chunk values calculated by a per-chunk compute. :l,ule
Examples are given below.
In LAMMPS, chunks are collections of atoms defined by a "compute
chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html
doc pages for details of how chunks can be defined and examples of how
they can be used to measure properties of a system.
For inputs that are computes, they must be a compute that calculates
per-chunk values. These are computes whose style names end in
"/chunk".
For inputs that are fixes, they should be a fix that calculates
per-chunk values. For example, "fix ave/chunk"_fix_ave_chunk.html or
"fix ave/time"_fix_ave_time.html (assuming it is time-averaging
per-chunk data).
For each atom, this compute accesses its chunk ID from the specified
{chunkID} compute, then accesses the per-chunk value in each input.
Those values are copied to this compute to become the output for that
atom.
The values generated by this compute will be 0.0 for atoms not in the
specified compute group {group-ID}. They will also be 0.0 if the atom
is not in a chunk, as assigned by the {chunkID} compute. They will
also be 0.0 if the current chunk ID for the atom is out-of-bounds with
respect to the number of chunks stored by a particular input compute
or fix.
NOTE: LAMMPS does not check that a compute or fix which calculates
per-chunk values uses the same definition of chunks as this compute.
It's up to you to be consistent. Likewise, for a fix input, LAMMPS
does not check that it is per-chunk data. It only checks that the fix
produces a global vector or array.
:line
Each listed input is operated on independently.
If a bracketed index I is used, it can be specified using a wildcard
asterisk with the index to effectively specify multiple values. This
takes the form "*" or "*n" or "n*" or "m*n". If N = the number of
columns in the array, then an asterisk with no numeric values means
all indices from 1 to N. A leading asterisk means all indices from 1
to n (inclusive). A trailing asterisk means all indices from n to N
(inclusive). A middle asterisk means all indices from m to n
(inclusive).
Using a wildcard is the same as if the individual columns of the array
had been listed one by one. E.g. these 2 compute chunk/spread/atom
commands are equivalent, since the "compute
com/chunk"_compute_com_chunk.html command creates a per-atom array
with 3 columns:
compute com all com/chunk mychunk
compute 10 all chunk/spread/atom mychunk c_com\[*\]
compute 10 all chunk/spread/atom mychunk c_com\[1\] c_com\[2\] c_com\[3\] :pre
:line
Here is an example of writing a dump file the with the center-of-mass
(COM) for the chunk each atom is in. The commands below can be added
to the bench/in.chain script.
compute cmol all chunk/atom molecule
compute com all com/chunk cmol
compute comchunk all chunk/spread/atom cmol c_com[*]
dump 1 all custom 50 tmp.dump id mol type x y z c_comchunk[*]
dump_modify 1 sort id :pre
The same per-chunk data for each atom could be used to define per-atom
forces for the "fix addforce"_fix_addforce.html command. In this
example the forces act to pull atoms of an extended polymer chain
towards its COM in an attractive manner.
compute prop all property/atom xu yu zu
variable k equal 0.1
variable fx atom v_k*(c_comchunk\[1\]-c_prop\[1\])
variable fy atom v_k*(c_comchunk\[2\]-c_prop\[2\])
variable fz atom v_k*(c_comchunk\[3\]-c_prop\[3\])
fix 3 all addforce v_fx v_fy v_fz :pre
Note that "compute property/atom"_compute_property_atom.html is used
to generate unwrapped coordinates for use in the per-atom force
calculation, so that the effect of periodic boundaries is accounted
for properly.
Over time this applied force could shrink each polymer chain's radius
of gyration in a polymer mixture simulation. Here is output from the
bench/in.chain script. Thermo output is shown for 1000 steps, where
the last column is the average radius of gyration over all 320 chains
in the 32000 atom system:
compute gyr all gyration/chunk cmol
variable ave equal ave(c_gyr)
thermo_style custom step etotal press v_ave :pre
0 22.394765 4.6721833 5.128278
100 22.445002 4.8166709 5.0348372
200 22.500128 4.8790392 4.9364875
300 22.534686 4.9183766 4.8590693
400 22.557196 4.9492211 4.7937849
500 22.571017 4.9161853 4.7412008
600 22.573944 5.0229708 4.6931243
700 22.581804 5.0541301 4.6440647
800 22.584683 4.9691734 4.6000016
900 22.59128 5.0247538 4.5611513
1000 22.586832 4.94697 4.5238362 :pre
:line
Here is an example for using one set of chunks, defined for molecules,
to compute the dipole moment vector for each chunk. E.g. for water
molecules. Then spreading those values to each atom in each chunk.
Then defining a second set of chunks based on spatial bins. And
finally, using the "fix ave/chunk"_fix_ave_chunk.html command to
calculate an average dipole moment vector per spatial bin.
compute cmol all chunk/atom molecule
compute dipole all dipole/chunk cmol
compute spread all chunk/spread/atom cmol c_dipole\[1\] c_dipole\[2\] c_dipole\[3\]
compute cspatial all chunk/atom bin/1d z lower 0.1 units reduced
fix ave all ave/chunk 100 10 1000 cspatial c_spread\[*\] :pre
Note that the "fix ave/chunk"_fix_ave_chunk.html command requires
per-atom values as input. That is why the compute chunk/spread/atom
command is used to assign per-chunk values to each atom in the chunk.
If a molecule straddles bin boundaries, each of its atoms contributes
in a weighted manner to the average dipole moment of the spatial bin
it is in.
:line
[Output info:]
This compute calculates a per-atom vector or array, which can be
accessed by any command that uses per-atom values from a compute as
input. See the "Howto output"_Howto_output.html doc page for an
overview of LAMMPS output options.
The output is a per-atom vector if a single input value is specified,
otherwise a per-atom array is output. The number of columns in the
array is the number of inputs provided. The per-atom values for the
vector or each column of the array will be in whatever
"units"_units.html the corresponding input value is in.
The vector or array values are "intensive".
[Restrictions:] none
[Related commands:]
"compute chunk/atom"_compute_chunk_atom.html, "fix
ave/chunk"_fix_ave_chunk.html, "compute
reduce/chunk"_compute_reduce_chunk.html
[Default:] none

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
compute dihedral/local command :h3
[Syntax:]
compute ID group-ID dihedral/local value1 value2 ... keyword args ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
dihedral/local = style name of this compute command :l
one or more values may be appended :l
value = {phi} or {v_name} :l
{phi} = tabulate dihedral angles
{v_name} = equal-style variable with name (see below) :pre
zero or more keyword/args pairs may be appended :l
keyword = {set} :l
{set} args = phi name
phi = only currently allowed arg
name = name of variable to set with phi :pre
:ule
[Examples:]
compute 1 all dihedral/local phi :pre
compute 1 all dihedral/local phi v_cos set phi p :pre
[Description:]
Define a computation that calculates properties of individual dihedral
interactions. The number of datums generated, aggregated across all
processors, equals the number of dihedral angles in the system, modified
by the group parameter as explained below.
The value {phi} is the dihedral angle, as defined in the diagram on
the "dihedral_style"_dihedral_style.html doc page.
The value {v_name} can be used together with the {set} keyword to
compute a user-specified function of the dihedral angle phi. The
{name} specified for the {v_name} value is the name of an "equal-style
variable"_variable.html which should evaluate a formula based on a
variable which will store the angle phi. This other variable must
be an "internal-style variable"_variable.html defined in the input
script; its initial numeric value can be anything. It must be an
internal-style variable, because this command resets its value
directly. The {set} keyword is used to identify the name of this
other variable associated with phi.
Note that the value of phi for each angle which stored in the internal
variable is in radians, not degrees.
As an example, these commands can be added to the bench/in.rhodo
script to compute the cosine and cosine^2 of every dihedral angle in
the system and output the statistics in various ways:
variable p internal 0.0
variable cos equal cos(v_p)
variable cossq equal cos(v_p)*cos(v_p) :pre
compute 1 all property/local datom1 datom2 datom3 datom4 dtype
compute 2 all dihedral/local phi v_cos v_cossq set phi p
dump 1 all local 100 tmp.dump c_1[*] c_2[*] :pre
compute 3 all reduce ave c_2[*]
thermo_style custom step temp press c_3[*] :pre
fix 10 all ave/histo 10 10 100 -1 1 20 c_2[2] mode vector file tmp.histo :pre
The "dump local"_dump.html command will output the angle,
cosine(angle), cosine^2(angle) for every dihedral in the system. The
"thermo_style"_thermo_style.html command will print the average of
those quantities via the "compute reduce"_compute_reduce.html command
with thermo output. And the "fix ave/histo"_fix_ave_histo.html
command will histogram the cosine(angle) values and write them to a
file.
:line
The local data stored by this command is generated by looping over all
the atoms owned on a processor and their dihedrals. A dihedral will
only be included if all 4 atoms in the dihedral are in the specified
compute group.
Note that as atoms migrate from processor to processor, there will be
no consistent ordering of the entries within the local vector or array
from one timestep to the next. The only consistency that is
guaranteed is that the ordering on a particular timestep will be the
same for local vectors or arrays generated by other compute commands.
For example, dihedral output from the "compute
property/local"_compute_property_local.html command can be combined
with data from this command and output by the "dump local"_dump.html
command in a consistent way.
Here is an example of how to do this:
compute 1 all property/local dtype datom1 datom2 datom3 datom4
compute 2 all dihedral/local phi
dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_1\[4\] c_1\[5\] c_2\[1\] :pre
[Output info:]
This compute calculates a local vector or local array depending on the
number of values. The length of the vector or number of rows in the
array is the number of dihedrals. If a single value is specified, a
local vector is produced. If two or more values are specified, a
local array is produced where the number of columns = the number of
values. The vector or array can be accessed by any command that uses
local values from a compute as input. See the "Howto
output"_Howto_output.html doc page for an overview of LAMMPS output
options.
The output for {phi} will be in degrees.
[Restrictions:] none
[Related commands:]
"dump local"_dump.html, "compute
property/local"_compute_property_local.html
[Default:] none

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
compute displace/atom command :h3
[Syntax:]
compute ID group-ID displace/atom :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
displace/atom = style name of this compute command :l
zero or more keyword/arg pairs may be appended :l
keyword = {refresh} :l
{replace} arg = name of per-atom variable :pre
:ule
[Examples:]
compute 1 all displace/atom
compute 1 all displace/atom refresh myVar :pre
[Description:]
Define a computation that calculates the current displacement of each
atom in the group from its original (reference) coordinates, including
all effects due to atoms passing through periodic boundaries.
A vector of four quantities per atom is calculated by this compute.
The first 3 elements of the vector are the dx,dy,dz displacements.
The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy +
dz*dz).
The displacement of an atom is from its original position at the time
the compute command was issued. The value of the displacement will be
0.0 for atoms not in the specified compute group.
NOTE: Initial coordinates are stored in "unwrapped" form, by using the
image flags associated with each atom. See the "dump
custom"_dump.html command for a discussion of "unwrapped" coordinates.
See the Atoms section of the "read_data"_read_data.html command for a
discussion of image flags and how they are set for each atom. You can
reset the image flags (e.g. to 0) before invoking this compute by
using the "set image"_set.html command.
NOTE: If you want the quantities calculated by this compute to be
continuous when running from a "restart file"_read_restart.html, then
you should use the same ID for this compute, as in the original run.
This is so that the fix this compute creates to store per-atom
quantities will also have the same ID, and thus be initialized
correctly with time=0 atom coordinates from the restart file.
:line
The {refresh} option can be used in conjunction with the "dump_modify
refresh" command to generate incremental dump files.
The definition and motivation of an incremental dump file is as
follows. Instead of outputting all atoms at each snapshot (with some
associated values), you may only wish to output the subset of atoms
with a value that has changed in some way compared to the value the
last time that atom was output. In some scenarios this can result in
a dramatically smaller dump file. If desired, by post-processing the
sequence of snapshots, the values for all atoms at all timesteps can
be inferred.
A concrete example using this compute, is a simulation of atom
diffusion in a solid, represented as atoms on a lattice. Diffusive
hops are rare. Imagine that when a hop occurs an atom moves more than
a distance {Dhop}. For any snapshot we only want to output atoms that
have hopped since the last snapshot. This can be accomplished with
something like the following commands:
write_dump all custom tmp.dump id type x y z # see comment below :pre
variable Dhop equal 0.6
variable check atom "c_dsp[4] > v_Dhop"
compute dsp all displace/atom refresh check
dump 1 all custom 100 tmp.dump id type x y z
dump_modify 1 append yes thresh c_dsp[4] > ${Dhop} &
refresh c_dsp delay 100 :pre
The "dump_modify thresh"_dump_modify.html command will only output
atoms that have displaced more than 0.6 Angstroms on each snapshot
(assuming metal units). The dump_modify {refresh} option triggers a
call to this compute at the end of every dump.
The {refresh} argument for this compute is the ID of an "atom-style
variable"_variable.html which calculates a Boolean value (0 or 1)
based on the same criterion used by dump_modify thresh. This compute
evaluates the atom-style variable. For each atom that returns 1
(true), the original (reference) coordinates of the atom (stored by
this compute) are updated.
The effect of these commands is that a particular atom will only be
output in the dump file on the snapshot after it makes a diffusive
hop. It will not be output again until it makes another hop.
Note that in the first snapshot of a subsequent run, no atoms will be
typically be output. That is because the initial displacement for all
atoms is 0.0. If an initial dump snapshot is desired, containing the
initial reference positions of all atoms, one way to do this is
illustrated above. An initial write_dump command can be used before
the first run. It will contain the positions of all the atoms,
Options in the "dump_modify"_dump_modify.html command above will
append new output to that same file and delay the output until a later
timestep. The {delay} setting avoids a second time = 0 snapshot which
would be empty.
:line
[Output info:]
This compute calculates a per-atom array with 4 columns, which can be
accessed by indices 1-4 by any command that uses per-atom values from
a compute as input. See the "Howto output"_Howto_output.html doc page
for an overview of LAMMPS output options.
The per-atom array values will be in distance "units"_units.html.
This compute supports the {refresh} option as explained above, for use
in conjunction with "dump_modify refresh"_dump_modify.html to generate
incremental dump files.
[Restrictions:] none
[Related commands:]
"compute msd"_compute_msd.html, "dump custom"_dump.html, "fix
store/state"_fix_store_state.html
[Default:] none

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
fix ave/chunk command :h3
[Syntax:]
fix ID group-ID ave/chunk Nevery Nrepeat Nfreq chunkID value1 value2 ... keyword args ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
ave/chunk = style name of this fix command :l
Nevery = use input values every this many timesteps :l
Nrepeat = # of times to use input values for calculating averages :l
Nfreq = calculate averages every this many timesteps :l
chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l
one or more input values can be listed :l
value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name :l
vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
density/number, density/mass = number or mass density
temp = temperature
c_ID = per-atom vector calculated by a compute with ID
c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
f_ID = per-atom vector calculated by a fix with ID
f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
v_name = per-atom vector calculated by an atom-style variable with name :pre
zero or more keyword/arg pairs may be appended :l
keyword = {norm} or {ave} or {bias} or {adof} or {cdof} or {file} or {overwrite} or {title1} or {title2} or {title3} :l
{norm} arg = {all} or {sample} or {none} = how output on {Nfreq} steps is normalized
all = output is sum of atoms across all {Nrepeat} samples, divided by atom count
sample = output is sum of {Nrepeat} sample averages, divided by {Nrepeat}
none = output is sum of {Nrepeat} sample sums, divided by {Nrepeat}
{ave} args = {one} or {running} or {window M}
one = output new average value every Nfreq steps
running = output cumulative average of all previous Nfreq steps
window M = output average of M most recent Nfreq steps
{bias} arg = bias-ID
bias-ID = ID of a temperature compute that removes a velocity bias for temperature calculation
{adof} value = dof_per_atom
dof_per_atom = define this many degrees-of-freedom per atom for temperature calculation
{cdof} value = dof_per_chunk
dof_per_chunk = define this many degrees-of-freedom per chunk for temperature calculation
{file} arg = filename
filename = file to write results to
{overwrite} arg = none = overwrite output file with only latest output
{format} arg = string
string = C-style format string
{title1} arg = string
string = text to print as 1st line of output file
{title2} arg = string
string = text to print as 2nd line of output file
{title3} arg = string
string = text to print as 3rd line of output file :pre
:ule
[Examples:]
fix 1 all ave/chunk 10000 1 10000 binchunk c_myCentro title1 "My output values"
fix 1 flow ave/chunk 100 10 1000 molchunk vx vz norm sample file vel.profile
fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running :pre
[NOTE:]
If you are trying to replace a deprecated fix ave/spatial command
with the newer, more flexible fix ave/chunk and "compute
chunk/atom"_compute_chunk_atom.html commands, you simply need to split
the fix ave/spatial arguments across the two new commands. For
example, this command:
fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile :pre
could be replaced by:
compute cc1 flow chunk/atom bin/1d y 0.0 1.0
fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile :pre
[Description:]
Use one or more per-atom vectors as inputs every few timesteps, sum
the values over the atoms in each chunk at each timestep, then average
the per-chunk values over longer timescales. The resulting chunk
averages can be used by other "output commands"_Howto_output.html such
as "thermo_style custom"_thermo_style.html, and can also be written to
a file.
In LAMMPS, chunks are collections of atoms defined by a "compute
chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
chunk/atom"_compute_chunk_atom.html doc page and the "Howto
chunk"_Howto_chunk.html doc page for details of how chunks can be
defined and examples of how they can be used to measure properties of
a system.
Note that only atoms in the specified group contribute to the summing
and averaging calculations. The "compute
chunk/atom"_compute_chunk_atom.html command defines its own group as
well as an optional region. Atoms will have a chunk ID = 0, meaning
they belong to no chunk, if they are not in that group or region.
Thus you can specify the "all" group for this command if you simply
want to use the chunk definitions provided by chunkID.
Each specified per-atom value can be an atom attribute (position,
velocity, force component), a mass or number density, or the result of
a "compute"_compute.html or "fix"_fix.html or the evaluation of an
atom-style "variable"_variable.html. In the latter cases, the
compute, fix, or variable must produce a per-atom quantity, not a
global quantity. Note that the "compute
property/atom"_compute_property_atom.html command provides access to
any attribute defined and stored by atoms. If you wish to
time-average global quantities from a compute, fix, or variable, then
see the "fix ave/time"_fix_ave_time.html command.
The per-atom values of each input vector are summed and averaged
independently of the per-atom values in other input vectors.
"Computes"_compute.html that produce per-atom quantities are those
which have the word {atom} in their style name. See the doc pages for
individual "fixes"_fix.html to determine which ones produce per-atom
quantities. "Variables"_variable.html of style {atom} are the only
ones that can be used with this fix since all other styles of variable
produce global quantities.
Note that for values from a compute or fix, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form "*" or "*n" or "n*" or
"m*n". If N = the size of the vector (for {mode} = scalar) or the
number of columns in the array (for {mode} = vector), then an asterisk
with no numeric values means all indices from 1 to N. A leading
asterisk means all indices from 1 to n (inclusive). A trailing
asterisk means all indices from n to N (inclusive). A middle asterisk
means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual columns of the array
had been listed one by one. E.g. these 2 fix ave/chunk commands are
equivalent, since the "compute
property/atom"_compute_property_atom.html command creates, in this
case, a per-atom array with 3 columns:
compute myAng all property/atom angmomx angmomy angmomz
fix 1 all ave/chunk 100 1 100 cc1 c_myAng\[*\] file tmp.angmom
fix 2 all ave/chunk 100 1 100 cc1 c_myAng\[1\] c_myAng\[2\] c_myAng\[3\] file tmp.angmom :pre
NOTE: This fix works by creating an array of size {Nchunk} by Nvalues
on each processor. {Nchunk} is the number of chunks which is defined
by the "compute chunk/atom"_compute_chunk_atom.html command.
Nvalues is the number of input values specified. Each processor loops
over its atoms, tallying its values to the appropriate chunk. Then
the entire array is summed across all processors. This means that
using a large number of chunks will incur an overhead in memory and
computational cost (summing across processors), so be careful to
define a reasonable number of chunks.
:line
The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what
timesteps the input values will be accessed and contribute to the
average. The final averaged quantities are generated on timesteps
that are a multiples of {Nfreq}. The average is over {Nrepeat}
quantities, computed in the preceding portion of the simulation every
{Nevery} timesteps. {Nfreq} must be a multiple of {Nevery} and
{Nevery} must be non-zero even if {Nrepeat} is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nrepeat*Nevery
can not exceed Nfreq.
For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
averaging is done; values are simply generated on timesteps
100,200,etc.
Each input value can also be averaged over the atoms in each chunk.
The way the averaging is done across the {Nrepeat} timesteps to
produce output on the {Nfreq} timesteps, and across multiple {Nfreq}
outputs, is determined by the {norm} and {ave} keyword settings, as
discussed below.
NOTE: To perform per-chunk averaging within a {Nfreq} time window, the
number of chunks {Nchunk} defined by the "compute
chunk/atom"_compute_chunk_atom.html command must remain constant. If
the {ave} keyword is set to {running} or {window} then {Nchunk} must
remain constant for the duration of the simulation. This fix forces
the chunk/atom compute specified by chunkID to hold {Nchunk} constant
for the appropriate time windows, by not allowing it to re-calculate
{Nchunk}, which can also affect how it assigns chunk IDs to atoms.
This is particularly important to understand if the chunks defined by
the "compute chunk/atom"_compute_chunk_atom.html command are spatial
bins. If its {units} keyword is set to {box} or {lattice}, then the
number of bins {Nchunk} and size of each bin will be fixed over the
{Nfreq} time window, which can affect which atoms are discarded if the
simulation box size changes. If its {units} keyword is set to
{reduced}, then the number of bins {Nchunk} will still be fixed, but
the size of each bin can vary at each timestep if the simulation box
size changes, e.g. for an NPT simulation.
:line
The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory.
As noted above, any other atom attributes can be used as input values
to this fix by using the "compute
property/atom"_compute_property_atom.html command and then specifying
an input value from that compute.
The {density/number} value means the number density is computed for
each chunk, i.e. number/volume. The {density/mass} value means the
mass density is computed for each chunk, i.e. total-mass/volume. The
output values are in units of 1/volume or density (mass/volume). See
the "units"_units.html command doc page for the definition of density
for each choice of units, e.g. gram/cm^3. If the chunks defined by
the "compute chunk/atom"_compute_chunk_atom.html command are spatial
bins, the volume is the bin volume. Otherwise it is the volume of the
entire simulation box.
The {temp} value means the temperature is computed for each chunk, by
the formula KE = DOF/2 k T, where KE = total kinetic energy of the
chunk of atoms (sum of 1/2 m v^2), DOF = the total number of degrees
of freedom for all atoms in the chunk, k = Boltzmann constant, and T =
temperature.
The DOF is calculated as N*adof + cdof, where N = number of atoms in
the chunk, adof = degrees of freedom per atom, and cdof = degrees of
freedom per chunk. By default adof = 2 or 3 = dimensionality of
system, as set via the "dimension"_dimension.html command, and cdof =
0.0. This gives the usual formula for temperature.
Note that currently this temperature only includes translational
degrees of freedom for each atom. No rotational degrees of freedom
are included for finite-size particles. Also no degrees of freedom
are subtracted for any velocity bias or constraints that are applied,
such as "compute temp/partial"_compute_temp_partial.html, or "fix
shake"_fix_shake.html or "fix rigid"_fix_rigid.html. This is because
those degrees of freedom (e.g. a constrained bond) could apply to sets
of atoms that are both included and excluded from a specific chunk,
and hence the concept is somewhat ill-defined. In some cases, you can
use the {adof} and {cdof} keywords to adjust the calculated degrees of
freedom appropriately, as explained below.
Also note that a bias can be subtracted from atom velocities before
they are used in the above formula for KE, by using the {bias}
keyword. This allows, for example, a thermal temperature to be
computed after removal of a flow velocity profile.
Note that the per-chunk temperature calculated by this fix and the
"compute temp/chunk"_compute_temp_chunk.html command can be different.
The compute calculates the temperature for each chunk for a single
snapshot. This fix 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. The compute allows the
center-of-mass velocity of each chunk to be subtracted before
calculating the temperature; this fix does not.
If a value begins with "c_", a compute ID must follow which has been
previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the compute is used. If a
bracketed integer is appended, the Ith column of the per-atom array
calculated by the compute is used. Users can also write code for
their own compute styles and "add them to LAMMPS"_Modify.html.
See the discussion above for how I can be specified with a wildcard
asterisk to effectively specify multiple values.
If a value begins with "f_", a fix ID must follow which has been
previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the fix is used. If a
bracketed integer is appended, the Ith column of the per-atom array
calculated by the fix is used. Note that some fixes only produce
their values on certain timesteps, which must be compatible with
{Nevery}, else an error results. Users can also write code for their
own fix styles and "add them to LAMMPS"_Modify.html. See the
discussion above for how I can be specified with a wildcard asterisk
to effectively specify multiple values.
If a value begins with "v_", a variable name must follow which has
been previously defined in the input script. Variables of style
{atom} can reference thermodynamic keywords and various per-atom
attributes, or invoke other computes, fixes, or variables when they
are evaluated, so this is a very general means of generating per-atom
quantities to average within chunks.
:line
Additional optional keywords also affect the operation of this fix
and its outputs.
The {norm} keyword affects how averaging is done for the per-chunk
values that are output every {Nfreq} timesteps.
It the {norm} setting is {all}, which is the default, a chunk value is
summed over all atoms in all {Nrepeat} samples, as is the count of
atoms in the chunk. The averaged output value for the chunk on the
{Nfreq} timesteps is Total-sum / Total-count. In other words it is an
average over atoms across the entire {Nfreq} timescale. For the
{density/number} and {density/mass} values, the volume (bin volume or
system volume) used in the final normalization will be the volume at
the final {Nfreq} timestep.
If the {norm} setting is {sample}, the chunk value is summed over
atoms for each sample, as is the count, and an "average sample value"
is computed for each sample, i.e. Sample-sum / Sample-count. The
output value for the chunk on the {Nfreq} timesteps is the average of
the {Nrepeat} "average sample values", i.e. the sum of {Nrepeat}
"average sample values" divided by {Nrepeat}. In other words it is an
average of an average. For the {density/number} and {density/mass}
values, the volume (bin volume or system volume) used in the
per-sample normalization will be the current volume at each sampling
step.
If the {norm} setting is {none}, a similar computation as for the
{sample} setting is done, except the individual "average sample
values" are "summed sample values". A summed sample value is simply
the chunk value summed over atoms in the sample, without dividing by
the number of atoms in the sample. The output value for the chunk on
the {Nfreq} timesteps is the average of the {Nrepeat} "summed sample
values", i.e. the sum of {Nrepeat} "summed sample values" divided by
{Nrepeat}. For the {density/number} and {density/mass} values, the
volume (bin volume or system volume) used in the per-sample sum
normalization will be the current volume at each sampling step.
The {ave} keyword determines how the per-chunk values produced every
{Nfreq} steps are averaged with values produced on previous steps that
were multiples of {Nfreq}, before they are accessed by another output
command or written to a file.
If the {ave} setting is {one}, which is the default, then the chunk
values produced on timesteps that are multiples of {Nfreq} are
independent of each other; they are output as-is without further
averaging.
If the {ave} setting is {running}, then the chunk values produced on
timesteps that are multiples of {Nfreq} are summed and averaged in a
cumulative sense before being output. Each output chunk value is thus
the average of the chunk value produced on that timestep with all
preceding values for the same chunk. This running average begins when
the fix is defined; it can only be restarted by deleting the fix via
the "unfix"_unfix.html command, or re-defining the fix by
re-specifying it.
If the {ave} setting is {window}, then the chunk values produced on
timesteps that are multiples of {Nfreq} are summed and averaged within
a moving "window" of time, so that the last M values for the same
chunk are used to produce the output. E.g. if M = 3 and Nfreq = 1000,
then the output on step 10000 will be the average of the individual
chunk values on steps 8000,9000,10000. Outputs on early steps will
average over less than M values if they are not available.
The {bias} keyword specifies the ID of a temperature compute that
removes a "bias" velocity from each atom, specified as {bias-ID}. It
is only used when the {temp} value is calculated, to compute the
thermal temperature of each chunk after the translational kinetic
energy components have been altered in a prescribed way, e.g. to
remove a flow velocity profile. See the doc pages for individual
computes that calculate a temperature to see which ones implement a
bias.
The {adof} and {cdof} keywords define the values used in the degree of
freedom (DOF) formula described above for temperature calculation
for each chunk. They are only used when the {temp} value is
calculated. They can be used to calculate a more appropriate
temperature for some kinds of chunks. Here are 3 examples:
If spatially binned chunks contain some number of water molecules and
"fix shake"_fix_shake.html is used to make each molecule rigid, then
you could calculate a temperature with 6 degrees of freedom (DOF) (3
translational, 3 rotational) per molecule by setting {adof} to 2.0.
If "compute temp/partial"_compute_temp_partial.html is used with the
{bias} keyword to only allow the x component of velocity to contribute
to the temperature, then {adof} = 1.0 would be appropriate.
If each chunk consists of a large molecule, with some number of its
bonds constrained by "fix shake"_fix_shake.html or the entire molecule
by "fix rigid/small"_fix_rigid.html, {adof} = 0.0 and {cdof} could be
set to the remaining degrees of freedom for the entire molecule
(entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid
molecule.
The {file} keyword allows a filename to be specified. Every {Nfreq}
timesteps, a section of chunk info will be written to a text file in
the following format. A line with the timestep and number of chunks
is written. Then one line per chunk is written, containing the chunk
ID (1-Nchunk), an optional original ID value, optional coordinate
values for chunks that represent spatial bins, the number of atoms in
the chunk, and one or more calculated values. More explanation of the
optional values is given below. The number of values in each line
corresponds to the number of values specified in the fix ave/chunk
command. The number of atoms and the value(s) are summed or average
quantities, as explained above.
The {overwrite} keyword will continuously overwrite the output file
with the latest output, so that it only contains one timestep worth of
output. This option can only be used with the {ave running} setting.
The {format} keyword sets the numeric format of each value when it is
printed to a file via the {file} keyword. Note that all values are
floating point quantities. The default format is %g. You can specify
a higher precision if desired, e.g. %20.16g.
The {title1} and {title2} and {title3} keywords allow specification of
the strings that will be printed as the first 3 lines of the output
file, assuming the {file} keyword was used. LAMMPS uses default
values for each of these, so they do not need to be specified.
By default, these header lines are as follows:
# Chunk-averaged data for fix ID and group name
# Timestep Number-of-chunks
# Chunk (OrigID) (Coord1) (Coord2) (Coord3) Ncount value1 value2 ... :pre
In the first line, ID and name are replaced with the fix-ID and group
name. The second line describes the two values that are printed at
the first of each section of output. In the third line the values are
replaced with the appropriate value names, e.g. fx or c_myCompute[2].
The words in parenthesis only appear with corresponding columns if the
chunk style specified for the "compute
chunk/atom"_compute_chunk_atom.html command supports them. The OrigID
column is only used if the {compress} keyword was set to {yes} for the
"compute chunk/atom"_compute_chunk_atom.html command. This means that
the original chunk IDs (e.g. molecule IDs) will have been compressed
to remove chunk IDs with no atoms assigned to them. Thus a compressed
chunk ID of 3 may correspond to an original chunk ID or molecule ID of
415. The OrigID column will list 415 for the 3rd chunk.
The CoordN columns only appear if a {binning} style was used in the
"compute chunk/atom"_compute_chunk_atom.html command. For {bin/1d},
{bin/2d}, and {bin/3d} styles the column values are the center point
of the bin in the corresponding dimension. Just Coord1 is used for
{bin/1d}, Coord2 is added for {bin/2d}, Coord3 is added for {bin/3d}.
For {bin/sphere}, just Coord1 is used, and it is the radial
coordinate. For {bin/cylinder}, Coord1 and Coord2 are used. Coord1
is the radial coordinate (away from the cylinder axis), and coord2 is
the coordinate along the cylinder axis.
Note that if the value of the {units} keyword used in the "compute
chunk/atom command"_compute_chunk_atom.html is {box} or {lattice}, the
coordinate values will be in distance "units"_units.html. If the
value of the {units} keyword is {reduced}, the coordinate values will
be in unitless reduced units (0-1). This is not true for the Coord1 value
of style {bin/sphere} or {bin/cylinder} which both represent radial
dimensions. Those values are always in distance "units"_units.html.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix computes a global array of values which can be accessed by
various "output commands"_Howto_output.html. The values can only be
accessed on timesteps that are multiples of {Nfreq} since that is when
averaging is performed. The global array has # of rows = the number
of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The # of columns =
M+1+Nvalues, where M = 1 to 4, depending on whether the optional
columns for OrigID and CoordN are used, as explained above. Following
the optional columns, the next column contains the count of atoms in
the chunk, and the remaining columns are the Nvalue quantities. When
the array is accessed with a row I that exceeds the current number of
chunks, than a 0.0 is returned by the fix instead of an error, since
the number of chunks can vary as a simulation runs depending on how
that value is computed by the compute chunk/atom command.
The array values calculated by this fix are treated as "intensive",
since they are typically already normalized by the count of atoms in
each chunk.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] none
[Related commands:]
"compute"_compute.html, "fix ave/atom"_fix_ave_atom.html, "fix
ave/histo"_fix_ave_histo.html, "fix ave/time"_fix_ave_time.html,
"variable"_variable.html, "fix ave/correlate"_fix_ave_correlate.html
[Default:]
The option defaults are norm = all, ave = one, bias = none, no file output, and
title 1,2,3 = strings as described above.

6
src/KSPACE/ewald_disp.cpp
View File

@ -178,6 +178,12 @@ void EwaldDisp::init()
if (!function[1] && !function[2]) dispersionflag = 0;
if (!function[3]) dipoleflag = 0;
// compute two charge force
two_charge();
// extract short-range Coulombic cutoff from pair style
pair_check();
// set accuracy (force units) from accuracy_relative or accuracy_absolute

12
src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
View File

@ -6,7 +6,7 @@ SHELL = /bin/sh
# compiler/linker settings
# specify flags and libraries needed for your compiler
KOKKOS_ABSOLUTE_PATH = /home/stefan/projects/lammps-mine/lib/kokkos
KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
export MPICH_CXX = $(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper
export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/bin/nvcc_wrapper
CC = mpicxx
@ -33,7 +33,7 @@ KOKKOS_ARCH = Kepler35
# LAMMPS ifdef settings
# see possible settings in Section 2.2 (step 4) of manual
LMP_INC = -DLAMMPS_GZIP -DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG
LMP_INC = -DLAMMPS_GZIP
# MPI library
# see discussion in Section 2.2 (step 5) of manual
@ -55,9 +55,9 @@ MPI_LIB =
# PATH = path for FFT library
# LIB = name of FFT library
FFT_INC = -I/usr/include/
FFT_PATH = -L/usr/lib/
FFT_LIB = -lfftw3
FFT_INC =
FFT_PATH =
FFT_LIB =
# JPEG and/or PNG library
# see discussion in Section 2.2 (step 7) of manual
@ -68,7 +68,7 @@ FFT_LIB = -lfftw3
JPG_INC =
JPG_PATH =
JPG_LIB = -ljpeg -lpng
JPG_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies

18
src/USER-MISC/fix_bond_react.cpp
View File

@ -2946,8 +2946,12 @@ void FixBondReact::read(int myrxn)
bondflag = 1;
readline(line);
sscanf(line,"%d",&ibonding[myrxn]);
if (ibonding[myrxn] > onemol->natoms)
error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
readline(line);
sscanf(line,"%d",&jbonding[myrxn]);
if (jbonding[myrxn] > onemol->natoms)
error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
} else if (strcmp(keyword,"EdgeIDs") == 0) {
EdgeIDs(line, myrxn);
} else if (strcmp(keyword,"Equivalences") == 0) {
@ -2987,6 +2991,8 @@ void FixBondReact::EdgeIDs(char *line, int myrxn)
for (int i = 0; i < nedge; i++) {
readline(line);
sscanf(line,"%d",&tmp);
if (tmp > onemol->natoms)
error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
edge[tmp-1][myrxn] = 1;
}
}
@ -2998,6 +3004,8 @@ void FixBondReact::Equivalences(char *line, int myrxn)
for (int i = 0; i < nequivalent; i++) {
readline(line);
sscanf(line,"%d %d",&tmp1,&tmp2);
if (tmp1 > onemol->natoms || tmp2 > onemol->natoms)
error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
//equivalences is-> clmn 1: post-reacted, clmn 2: pre-reacted
equivalences[tmp2-1][0][myrxn] = tmp2;
equivalences[tmp2-1][1][myrxn] = tmp1;
@ -3017,6 +3025,8 @@ void FixBondReact::CustomEdges(char *line, int myrxn)
for (int i = 0; i < ncustom; i++) {
readline(line);
sscanf(line,"%d %s",&tmp,edgemode);
if (tmp > onemol->natoms)
error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
if (strcmp(edgemode,"none") == 0)
custom_edges[tmp-1][myrxn] = 0;
else if (strcmp(edgemode,"charges") == 0)
@ -3033,6 +3043,8 @@ void FixBondReact::DeleteAtoms(char *line, int myrxn)
for (int i = 0; i < ndelete; i++) {
readline(line);
sscanf(line,"%d",&tmp);
if (tmp > onemol->natoms)
error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
delete_atoms[tmp-1][myrxn] = 1;
}
}
@ -3043,6 +3055,8 @@ void FixBondReact::ChiralCenters(char *line, int myrxn)
for (int i = 0; i < nchiral; i++) {
readline(line);
sscanf(line,"%d",&tmp);
if (tmp > onemol->natoms)
error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
chiral_atoms[tmp-1][0][myrxn] = 1;
if (onemol->xflag == 0)
error->one(FLERR,"Bond/react: Molecule template 'Coords' section required for chiralIDs keyword");
@ -3080,6 +3094,8 @@ void FixBondReact::Constraints(char *line, int myrxn)
if (strcmp(constraint_type,"distance") == 0) {
constraints[nconstraints][1] = DISTANCE;
sscanf(line,"%*s %lg %lg %lg %lg",&tmp[0],&tmp[1],&tmp[2],&tmp[3]);
if (tmp[0] > onemol->natoms || tmp[1] > onemol->natoms)
error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
constraints[nconstraints][2] = tmp[0];
constraints[nconstraints][3] = tmp[1];
constraints[nconstraints][4] = tmp[2]*tmp[2]; // using square of distance
@ -3087,6 +3103,8 @@ void FixBondReact::Constraints(char *line, int myrxn)
} else if (strcmp(constraint_type,"angle") == 0) {
constraints[nconstraints][1] = ANGLE;
sscanf(line,"%*s %lg %lg %lg %lg %lg",&tmp[0],&tmp[1],&tmp[2],&tmp[3],&tmp[4]);
if (tmp[0] > onemol->natoms || tmp[1] > onemol->natoms || tmp[2] > onemol->natoms)
error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
constraints[nconstraints][2] = tmp[0];
constraints[nconstraints][3] = tmp[1];
constraints[nconstraints][4] = tmp[2];

4
src/USER-MISC/fix_bond_react.h
View File

@ -232,6 +232,10 @@ E: Bond/react: Unknown section in map file
Please ensure reaction map files are properly formatted.
E: Bond/react: Invalid template atom ID in map file
Atom IDs in molecule templates range from 1 to the number of atoms in the template.
E or W: Bond/react: Atom affected by reaction %s too close to template edge
This means an atom which changes type or connectivity during the

14
src/compute_global_atom.cpp
View File

@ -233,10 +233,6 @@ ComputeGlobalAtom::ComputeGlobalAtom(LAMMPS *lmp, int narg, char **arg) :
else size_peratom_cols = nvalues;
nmax = maxvector = 0;
indices = NULL;
varatom = NULL;
vecglobal = NULL;
vector_atom = NULL;
array_atom = NULL;
}
@ -320,6 +316,10 @@ void ComputeGlobalAtom::compute_peratom()
nmax = atom->nmax;
memory->destroy(indices);
memory->create(indices,nmax,"global/atom:indices");
if (whichref == VARIABLE) {
memory->destroy(varatom);
memory->create(varatom,nmax,"global/atom:varatom");
}
if (nvalues == 1) {
memory->destroy(vector_atom);
memory->create(vector_atom,nmax,"global/atom:vector_atom");
@ -377,12 +377,6 @@ void ComputeGlobalAtom::compute_peratom()
}
} else if (whichref == VARIABLE) {
if (atom->nmax > nmax) {
nmax = atom->nmax;
memory->destroy(varatom);
memory->create(varatom,nmax,"global/atom:varatom");
}
input->variable->compute_atom(ref2index,igroup,varatom,1,0);
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)

2
src/image.cpp
View File

@ -1466,10 +1466,12 @@ double *Image::color2rgb(const char *color, int index)
return userrgb[-index-1];
}
if (color) {
for (int i = 0; i < ncolors; i++)
if (strcmp(color,username[i]) == 0) return userrgb[i];
for (int i = 0; i < NCOLORS; i++)
if (strcmp(color,name[i]) == 0) return rgb[i];
}
return NULL;
}