From dddce90b0cee3295099278bbafc3ecdace1d2a6c Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 1 Apr 2015 00:21:56 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13352 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_deposit.html | 28 ++++++++++------- doc/fix_deposit.txt | 26 ++++++++++------ doc/fix_rigid.html | 69 ++++++++++++++++++++++-------------------- doc/fix_rigid.txt | 71 ++++++++++++++++++++++++-------------------- doc/group.html | 4 +-- doc/group.txt | 4 +-- doc/molecule.html | 8 ++--- doc/molecule.txt | 8 ++--- 8 files changed, 123 insertions(+), 95 deletions(-) diff --git a/doc/fix_deposit.html b/doc/fix_deposit.html index 4eff588228..93a498194a 100644 --- a/doc/fix_deposit.html +++ b/doc/fix_deposit.html @@ -162,8 +162,8 @@ shake command which also appears in your input script.

Each timestep a particle is inserted, the coordinates for its atoms are chosen as follows. For insertion of individual atoms, the "position" referred to in the following description is the coordinate -of the atom. For insertion of molecule, the "position is the -geometric center of the molecule; see the (molecule doc +of the atom. For insertion of molecule, the "position" is the +geometric center of the molecule; see the molecule doc page for details. A random rotation of the molecule around its center point is performed, which determines the coordinates all the individual atoms. @@ -183,14 +183,22 @@ particles is less than the delta setting.

Once a trial x,y,z position has been selected, the insertion is only performed if no current atom in the simulation is within a distance R of any atom in the new particle, including the effect of periodic -boundary conditions if applicable. Note that the default value for R -is 0.0, which will allow atoms to strongly overlap if you are -inserting where other atoms are present. This distance test is -performed independently for each atom in an inserted molecule, based -on the randomly rotated configuration of the molecule. If this test -fails, a new random position within the insertion volume is chosen and -another trial is made. Up to Q attempts are made. If the particle is -not successfully inserted, LAMMPS prints a warning message. +boundary conditions if applicable. R is defined by the near +keyword. Note that the default value for R is 0.0, which will allow +atoms to strongly overlap if you are inserting where other atoms are +present. This distance test is performed independently for each atom +in an inserted molecule, based on the randomly rotated configuration +of the molecule. If this test fails, a new random position within the +insertion volume is chosen and another trial is made. Up to Q +attempts are made. If the particle is not successfully inserted, +LAMMPS prints a warning message. +

+

IMPORTANT NOTE: If you are inserting finite size particles or a +molecule or rigid body consisting of finite-size particles, then you +should typically set R larger than the distance at which any inserted +particle may overlap with either a previouly inserted particle or an +existing particle. LAMMPS will issue a warning if R is smaller than +this value, based on the radii of existing and inserted particles.

The rate option moves the insertion volume in the z direction (3d) or y direction (2d). This enables particles to be inserted from a diff --git a/doc/fix_deposit.txt b/doc/fix_deposit.txt index 0881bff5f2..ee86cec892 100644 --- a/doc/fix_deposit.txt +++ b/doc/fix_deposit.txt @@ -151,7 +151,7 @@ Each timestep a particle is inserted, the coordinates for its atoms are chosen as follows. For insertion of individual atoms, the "position" referred to in the following description is the coordinate of the atom. For insertion of molecule, the "position" is the -geometric center of the molecule; see the (molecule"_molecule.html doc +geometric center of the molecule; see the "molecule"_molecule.html doc page for details. A random rotation of the molecule around its center point is performed, which determines the coordinates all the individual atoms. @@ -171,14 +171,22 @@ particles is less than the {delta} setting. Once a trial x,y,z position has been selected, the insertion is only performed if no current atom in the simulation is within a distance R of any atom in the new particle, including the effect of periodic -boundary conditions if applicable. Note that the default value for R -is 0.0, which will allow atoms to strongly overlap if you are -inserting where other atoms are present. This distance test is -performed independently for each atom in an inserted molecule, based -on the randomly rotated configuration of the molecule. If this test -fails, a new random position within the insertion volume is chosen and -another trial is made. Up to Q attempts are made. If the particle is -not successfully inserted, LAMMPS prints a warning message. +boundary conditions if applicable. R is defined by the {near} +keyword. Note that the default value for R is 0.0, which will allow +atoms to strongly overlap if you are inserting where other atoms are +present. This distance test is performed independently for each atom +in an inserted molecule, based on the randomly rotated configuration +of the molecule. If this test fails, a new random position within the +insertion volume is chosen and another trial is made. Up to Q +attempts are made. If the particle is not successfully inserted, +LAMMPS prints a warning message. + +IMPORTANT NOTE: If you are inserting finite size particles or a +molecule or rigid body consisting of finite-size particles, then you +should typically set R larger than the distance at which any inserted +particle may overlap with either a previouly inserted particle or an +existing particle. LAMMPS will issue a warning if R is smaller than +this value, based on the radii of existing and inserted particles. The {rate} option moves the insertion volume in the z direction (3d) or y direction (2d). This enables particles to be inserted from a diff --git a/doc/fix_rigid.html b/doc/fix_rigid.html index 33b34c9673..8bb512edbe 100644 --- a/doc/fix_rigid.html +++ b/doc/fix_rigid.html @@ -129,7 +129,7 @@ ensemble, as described below. rigid/small. The NVE/NVT/NPT/NHT versions belong to one of the two variants, as their style names indicate.

-

IMPORTANT NOTE: Not all of the bodystyle options and keyword/value +

IMPORTANT NOTE: Not all of the bodystyle options and keyword/value options are available for both the rigid and rigid/small variants. See details below.

@@ -183,6 +183,8 @@ command), setting the force on them to 0.0 (via the fix nve command).

+

NOTE: edit this +

IMPORTANT NOTE: The aggregate properties of each rigid body are calculated at the start of each simulation run. These include its center of mass, moments of inertia, and net velocity and angular @@ -201,9 +203,9 @@ via several options.

IMPORTANT NOTE: With fix rigid/small, which requires bodystyle molecule, you can define a system that has no rigid bodies -initially. This is useful when you are adding rigid bodies on-the-fly -via commands such as fix deposit or fix -pour. +initially. This is useful when you are using the mol keyword in +conjunction with another fix that is adding rigid bodies on-the-fly, +such as fix deposit or fix pour.

For bodystyle single the entire fix group of atoms is treated as one rigid body. This option is only allowed for fix rigid and its @@ -471,17 +473,25 @@ associated with the fix rigid commands.

-

The mol keyword can only be used with fix rigid/small. It should be +

The mol keyword can only be used with fix rigid/small. It must be used when other commands, such as fix deposit or fix pour, add rigid bodies on-the-fly during a simulation. You specify a template-ID previously defined using the molecule command, which reads a file that defines the -molecule. You must use the same template-ID that the command adding -rigid bodies uses. The coordinates, atom types, atom diameters, -center-of-mass, and moments of inertia can be specified in the -molecule file. See the molecule command for details. -The only settings required to be in this file are the coordinates and -types of atoms in the molecule. +molecule. You must use the same template-ID that the other fix +which is adding rigid bodies uses. The coordinates, atom types, atom +diameters, center-of-mass, and moments of inertia can be specified in +the molecule file. See the molecule command for +details. The only settings required to be in this file are the +coordinates and types of atoms in the molecule, in which case the +molecule command calculates the other quantities itself. +

+

Note that these other fixes create new rigid bodies, in addition to +those defined initially by this fix via the bodystyle setting. +

+

Also note that when using the mol keyword, extra restart information +about all rigid bodies is written out whenever a restart file is +written out. See the IMPORTANT NOTE in the next section for details.

@@ -505,6 +515,8 @@ comment lines starting with "#" which are ignored. The first non-blank, non-comment line should list N = the number of lines to follow. The N successive lines contain the following information:

+

NOTE: edit this +

ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
 ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
 ...
@@ -528,26 +540,16 @@ the simulation box XYZ axes, not with respect to the prinicpal axes of
 the rigid body itself.  LAMMPS performs the latter calculation
 internally.
 

-
IMPORTANT NOTE: If you use the infile keyword and write restart
-files during a simulation, then each time a restart file is written,
-the fix also write an auxiliary restart file with the name
+
IMPORTANT NOTE: If you use the infile or mol keywords and write
+restart files during a simulation, then each time a restart file is
+written, the fix also write an auxiliary restart file with the name
 rfile.rigid, where "rfile" is the name of the restart file,
 e.g. tmp.restart.10000 and tmp.restart.10000.rigid.  This auxiliary
-file is in the same format described above and contains info on the
-current center-of-mass and 6 moments of inertia.  Thus it can be used
-in a new input script that restarts the run and re-specifies a rigid
-fix using an infile keyword and the appropriate filename.  Note that
-the auxiliary file will contain one line for every rigid body, even if
-the original file only listed a subset of the rigid bodies.
-

-
IMPORTANT NOTE: If you are using fix rigid/small and defining a system
-that has no rigid bodies initially, because they will be added
-on-the-fly by commands such as fix deposit or fix
-pour, you may still wish to use the infile keyword.
-This is so that restart files written during the simulation will
-output an auxiliary restart file as described above with information
-on the new rigid bodies.  In this case the initial infile file
-should use N = 0.
+file is in the same format described above.  Thus it can be used in a
+new input script that restarts the run and re-specifies a rigid fix
+using an infile keyword and the appropriate filename.  Note that the
+auxiliary file will contain one line for every rigid body, even if the
+original file only listed a subset of the rigid bodies.
 

 

 
@@ -656,9 +658,12 @@ more instructions on how to use the accelerated styles effectively.
 
Restart, fix_modify, output, run start/stop, minimize info:
 

 
No information about the rigid and rigid/small and rigid/nve
-fixes are written to binary restart files.  For style
-rigid/nvt the state of the Nose/Hoover thermostat is written to
-binary restart files.  See the
+fixes are written to binary restart files.  The
+exception is if the infile or mol keyword is used, in which case
+an auxiliary file is written out with rigid body information each time
+a restart file is written, as explained above for the infile
+keyword.  For style rigid/nvt the state of the Nose/Hoover
+thermostat is written to binary restart files.  See the
 read_restart command for info on how to re-specify
 a fix in an input script that reads a restart file, so that the
 operation of the fix continues in an uninterrupted fashion.
diff --git a/doc/fix_rigid.txt b/doc/fix_rigid.txt
index 1530245211..277e4105e8 100644
--- a/doc/fix_rigid.txt
+++ b/doc/fix_rigid.txt
@@ -111,7 +111,7 @@ There are two main variants of this fix, fix rigid and fix
 rigid/small.  The NVE/NVT/NPT/NHT versions belong to one of the two
 variants, as their style names indicate.  
 
-IMPORTANT NOTE: Not all of the bodystyle options and keyword/value
+IMPORTANT NOTE: Not all of the {bodystyle} options and keyword/value
 options are available for both the {rigid} and {rigid/small} variants.
 See details below.
 
@@ -165,6 +165,10 @@ command), setting the force on them to 0.0 (via the "fix
 setforce"_fix_setforce.html command), and integrating them as usual
 (e.g. via the "fix nve"_fix_nve.html command).
 
+
+NOTE: edit this
+
+
 IMPORTANT NOTE: The aggregate properties of each rigid body are
 calculated at the start of each simulation run.  These include its
 center of mass, moments of inertia, and net velocity and angular
@@ -183,9 +187,9 @@ via several options.
 
 IMPORTANT NOTE: With fix rigid/small, which requires bodystyle
 {molecule}, you can define a system that has no rigid bodies
-initially.  This is useful when you are adding rigid bodies on-the-fly
-via commands such as "fix deposit"_fix_deposit.html or "fix
-pour"_fix_pour.html.
+initially.  This is useful when you are using the {mol} keyword in
+conjunction with another fix that is adding rigid bodies on-the-fly,
+such as "fix deposit"_fix_deposit.html or "fix pour"_fix_pour.html.
 
 For bodystyle {single} the entire fix group of atoms is treated as one
 rigid body.  This option is only allowed for fix rigid and its
@@ -453,17 +457,25 @@ associated with the fix rigid commands.
 
 :line
 
-The {mol} keyword can only be used with fix rigid/small.  It should be
+The {mol} keyword can only be used with fix rigid/small.  It must be
 used when other commands, such as "fix deposit"_fix_deposit.html or
 "fix pour"_fix_pour.html, add rigid bodies on-the-fly during a
 simulation.  You specify a {template-ID} previously defined using the
 "molecule"_molecule.html command, which reads a file that defines the
-molecule.  You must use the same {template-ID} that the command adding
-rigid bodies uses.  The coordinates, atom types, atom diameters,
-center-of-mass, and moments of inertia can be specified in the
-molecule file.  See the "molecule"_molecule.html command for details.
-The only settings required to be in this file are the coordinates and
-types of atoms in the molecule.
+molecule.  You must use the same {template-ID} that the other fix
+which is adding rigid bodies uses.  The coordinates, atom types, atom
+diameters, center-of-mass, and moments of inertia can be specified in
+the molecule file.  See the "molecule"_molecule.html command for
+details.  The only settings required to be in this file are the
+coordinates and types of atoms in the molecule, in which case the
+molecule command calculates the other quantities itself.
+
+Note that these other fixes create new rigid bodies, in addition to
+those defined initially by this fix via the {bodystyle} setting.
+
+Also note that when using the {mol} keyword, extra restart information
+about all rigid bodies is written out whenever a restart file is
+written out.  See the IMPORTANT NOTE in the next section for details.
 
 :line
 
@@ -487,6 +499,8 @@ comment lines starting with "#" which are ignored.  The first
 non-blank, non-comment line should list N = the number of lines to
 follow.  The N successive lines contain the following information:
 
+NOTE: edit this
+
 ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
 ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz
 ...
@@ -510,26 +524,16 @@ the simulation box XYZ axes, not with respect to the prinicpal axes of
 the rigid body itself.  LAMMPS performs the latter calculation
 internally.
 
-IMPORTANT NOTE: If you use the {infile} keyword and write restart
-files during a simulation, then each time a restart file is written,
-the fix also write an auxiliary restart file with the name
+IMPORTANT NOTE: If you use the {infile} or {mol} keywords and write
+restart files during a simulation, then each time a restart file is
+written, the fix also write an auxiliary restart file with the name
 rfile.rigid, where "rfile" is the name of the restart file,
 e.g. tmp.restart.10000 and tmp.restart.10000.rigid.  This auxiliary
-file is in the same format described above and contains info on the
-current center-of-mass and 6 moments of inertia.  Thus it can be used
-in a new input script that restarts the run and re-specifies a rigid
-fix using an {infile} keyword and the appropriate filename.  Note that
-the auxiliary file will contain one line for every rigid body, even if
-the original file only listed a subset of the rigid bodies.
-
-IMPORTANT NOTE: If you are using fix rigid/small and defining a system
-that has no rigid bodies initially, because they will be added
-on-the-fly by commands such as "fix deposit"_fix_deposit.html or "fix
-pour"_fix_pour.html, you may still wish to use the {infile} keyword.
-This is so that restart files written during the simulation will
-output an auxiliary restart file as described above with information
-on the new rigid bodies.  In this case the initial {infile} file
-should use N = 0.
+file is in the same format described above.  Thus it can be used in a
+new input script that restarts the run and re-specifies a rigid fix
+using an {infile} keyword and the appropriate filename.  Note that the
+auxiliary file will contain one line for every rigid body, even if the
+original file only listed a subset of the rigid bodies.
 
 :line
 
@@ -638,9 +642,12 @@ more instructions on how to use the accelerated styles effectively.
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
 No information about the {rigid} and {rigid/small} and {rigid/nve}
-fixes are written to "binary restart files"_restart.html.  For style
-{rigid/nvt} the state of the Nose/Hoover thermostat is written to
-"binary restart files"_restart.html.  See the
+fixes are written to "binary restart files"_restart.html.  The
+exception is if the {infile} or {mol} keyword is used, in which case
+an auxiliary file is written out with rigid body information each time
+a restart file is written, as explained above for the {infile}
+keyword.  For style {rigid/nvt} the state of the Nose/Hoover
+thermostat is written to "binary restart files"_restart.html.  See the
 "read_restart"_read_restart.html command for info on how to re-specify
 a fix in an input script that reads a restart file, so that the
 operation of the fix continues in an uninterrupted fashion.
diff --git a/doc/group.html b/doc/group.html
index 6f1b149f70..c2fca7b398 100644
--- a/doc/group.html
+++ b/doc/group.html
@@ -254,9 +254,9 @@ variable        rad equal 18-(step/v_nsteps)*(18-5)
 region          ss sphere 20 20 0 v_rad
 group           mobile dynamic all region ss
 fix             1 mobile nve
-run             $nsteps
+run             ${nsteps}
 group           mobile static
-run	        $nsteps 
+run	        ${nsteps}

IMPORTANT NOTE: All fixes and computes take a group ID as an argument, but they do not all allow for use of a dynamic group. If you get an diff --git a/doc/group.txt b/doc/group.txt index fd5d6a2a77..5619698e5c 100644 --- a/doc/group.txt +++ b/doc/group.txt @@ -250,9 +250,9 @@ variable rad equal 18-(step/v_nsteps)*(18-5) region ss sphere 20 20 0 v_rad group mobile dynamic all region ss fix 1 mobile nve -run ${nsteps} +run $\{nsteps\} group mobile static -run ${nsteps} :pre +run $\{nsteps\} :pre IMPORTANT NOTE: All fixes and computes take a group ID as an argument, but they do not all allow for use of a dynamic group. If you get an diff --git a/doc/molecule.html b/doc/molecule.html index 46c1cf3469..84b5db8633 100644 --- a/doc/molecule.html +++ b/doc/molecule.html @@ -1,5 +1,5 @@ -

LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
<LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands
@@ -97,9 +97,9 @@ appear if the value(s) are different than the default.

For mass, com, and inertia, the default is for LAMMPS to calculate this quantity itself if needed, assuming the molecules -consists of a set of point particles. You typically only need to -specify these values for a rigid body consisting of overlapping -finite-size particles. +consists of a set of point particles. You only need to specify these +values for a rigid body consisting of finite-size particles, +especially if they are overlapping.

The mass and center-of-mass coordinates (Xc,Yc,Zc) are self-explanatory. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) diff --git a/doc/molecule.txt b/doc/molecule.txt index f437222851..9d029bfc4d 100644 --- a/doc/molecule.txt +++ b/doc/molecule.txt @@ -1,4 +1,4 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c +<"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) @@ -94,9 +94,9 @@ Ixx Iyy Izz Ixy Ixz Iyz {inertia} = 6 components of inertia tensor of molecule : For {mass}, {com}, and {inertia}, the default is for LAMMPS to calculate this quantity itself if needed, assuming the molecules -consists of a set of point particles. You typically only need to -specify these values for a rigid body consisting of overlapping -finite-size particles. +consists of a set of point particles. You only need to specify these +values for a rigid body consisting of finite-size particles, +especially if they are overlapping. The mass and center-of-mass coordinates (Xc,Yc,Zc) are self-explanatory. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)