From 05968b3cd2951fe5fc451d758271cee9df78409f Mon Sep 17 00:00:00 2001 From: sjplimp Date: Sat, 4 Sep 2010 00:17:54 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4687 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 4 +- doc/Section_commands.txt | 4 +- doc/pair_reax.html | 96 +++++++++++++++++++++----------------- doc/pair_reax.txt | 97 +++++++++++++++++++++------------------ 4 files changed, 111 insertions(+), 90 deletions(-) diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 6ea758639c..c4c098ae64 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -340,7 +340,7 @@ of each style or click on the style itself for a full description:

-
atcimdlangevin/effnph/effnpt/effnve/eff
nvt/effnvt/sllod/effsmdtemp/rescale/eff +
nvt/effnvt/sllod/effqeq/reaxsmdtemp/rescale/eff
@@ -398,7 +398,7 @@ potentials. Click on the style itself for a full description:

-
buck/coulcg/cmmcg/cmm/coul/cutcg/cmm/coul/long
eam/cdeff/cutlj/coul +
eam/cdeff/cutlj/coulreax/c
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 0897d857bd..377ec3d5d6 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -470,6 +470,7 @@ These are fix styles contributed by users, which can be used if "nve/eff"_fix_nve_eff.html, "nvt/eff"_fix_nh_eff.html, "nvt/sllod/eff"_fix_nvt_sllod_eff.html, +"qeq/reax"_fix_qeq_reax.html, "smd"_fix_smd.html, "temp/rescale/eff"_fix_temp_rescale_eff.html :tb(c=6,ea=c) @@ -613,7 +614,8 @@ These are pair styles contributed by users, which can be used if "cg/cmm/coul/long"_pair_cmm.html, "eam/cd"_pair_eam.html, "eff/cut"_pair_eff.html, -"lj/coul"_pair_lj_coul.html :tb(c=4,ea=c) +"lj/coul"_pair_lj_coul.html, +"reax/c"_pair_reax_c.html :tb(c=4,ea=c) :line diff --git a/doc/pair_reax.html b/doc/pair_reax.html index 4c304e2445..0c572f840d 100644 --- a/doc/pair_reax.html +++ b/doc/pair_reax.html @@ -27,26 +27,38 @@ pair_coeff * * ffield.reax 3 NULL NULL 3

Description:

-

The pair style computes the ReaxFF potential of van Duin, Goddard and +

Style reax computes the ReaxFF potential of van Duin, Goddard and co-workers. ReaxFF uses distance-dependent bond-order functions to represent the contributions of chemical bonding to the potential -energy. There is more than one version of ReaxFF. The version implemented -in LAMMPS uses the functional forms documented in the -supplemental information of the following paper: (Chenoweth et al., - 2008). +energy. There is more than one version of ReaxFF. The version +implemented in LAMMPS uses the functional forms documented in the +supplemental information of the following paper: +(Chenoweth). The version integrated into LAMMPS matches +the most up-to-date version of ReaxFF as of summer 2010.

-

LAMMPS requires that a file called ffield.reax be provided, containing the -ReaxFF parameters for each atom type, bond type, etc. The format is identical to -the ffield file used by van Duin and co-workers. The filename is also -reuqired as an argument in the pair_coeff command. Any value other than -ffield.reax will be rejected (see below). +

The reax style differs from the pair_style reax/c +command in the lo-level implementation details. The reax style is a +Fortran library, linked to LAMMPS. The reax/c style was initially +implemented as stand-alone C code and is now integrated into LAMMPS as +a package.

-

LAMMPS provides several different versions of ffield.reax -in its potentials dir, each called potentials/ffield.reax.label. -These are documented in potentials/README.reax. -The default ffield.reax contains parameterizations for the following -elements: C, H, O, N, S. You can use one of the other files in place of it, -or obtain a file from elsewhere. +

LAMMPS requires that a file called ffield.reax be provided, containing +the ReaxFF parameters for each atom type, bond type, etc. The format +is identical to the ffield file used by van Duin and co-workers. The +filename is required as an argument in the pair_coeff command. Any +value other than "ffield.reax" will be rejected (see below). +

+

LAMMPS provides several different versions of ffield.reax in its +potentials dir, each called potentials/ffield.reax.label. These are +documented in potentials/README.reax. The default ffield.reax +contains parameterizations for the following elements: C, H, O, N, S. +

+

The format of these files is identical to that used originally by van +Duin. We have tested the accuracy of pair_style reax/c potential +against the original ReaxFF code for the systems mentioned above. You +can use other ffield files for specific chemical systems that may be +available elsewhere (but note that their accuracy may not have been +tested).

The hbcut and precision settings are optional arguments. If neither is provided, default settings are used: hbcut = 10 (which is @@ -55,9 +67,10 @@ If you wish to override either of these defaults, then both settings must be specified.

Use of this pair style requires that a charge be defined for every -atom since the potential performs charge equilibration. See the -atom_style and read_data commands -for details on how to specify charges. +atom since the reax pair style performs a charge equilibration (QEq) +calculation. See the atom_style and +read_data commands for details on how to specify +charges.

The thermo variable evdwl stores the sum of all the ReaxFF potential energy contributions, with the exception of the Coulombic and charge @@ -86,25 +99,24 @@ file into the directory you are running from. If you wish to use another ReaxFF potential file, then name it "ffield.reax" and put it in the directory you run from.

-

In the ReaxFF potential file, near the top, is a section that contains -element names, each with a couple dozen numeric parameters. The -default ffield.reax provided with LAMMPS lists 5 elements: C, H, O, N, -S. Think of these as numbered 1 to 5. When using this file each of -the N indices you specify for the N atom types of LAMMPS atoms must be -an integer from 1 to 5. Atoms with LAMMPS type 1 will be mapped to -whatever element you specify as the first index value, etc. If a -mapping value is specified as NULL, the mapping is not performed. -This can be used when a ReaxFF potential is used as part of the -hybrid pair style. The NULL values are placeholders for atom types -that will be used with other potentials. +

In the ReaxFF potential file, near the top, after the general +parameters, is the atomic parameters section that contains element +names, each with a couple dozen numeric parameters. If there are M +elements specified in the ffield file, think of these as numbered 1 +to M. Each of the N indices you specify for the N atom types of LAMMPS +atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will +be mapped to whatever element you specify as the first index value, +etc. If a mapping value is specified as NULL, the mapping is not +performed. This can be used when a ReaxFF potential is used as part +of the hybrid pair style. The NULL values are placeholders for atom +types that will be used with other potentials.

-

In the pair_coeff example above with 3 1 2 2, the LAMMPS simulation -has 4 atoms types and they are set as follows: +

As an example, say your LAMMPS simulation has 4 atom types and the +elements are ordered as C, H, O, N in the ffield file. If you want +the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be +H, you would use the following pair_coeff command:

-
type 1 = O
-type 2 = C
-type 3 = H
-type 4 = H 
+
pair_coeff * * ffield.reax 1 1 4 2 
 

 

 
@@ -129,17 +141,15 @@ LAMMPS was built with that package, which also requires the REAX
 library be built and linked with LAMMPS.  See the Making
 LAMMPS section for more info.
 

-
The ffield.reax potential file provided with LAMMPS in the potentials
-directory is parameterized for real units.  You can use
+
The ReaxFF potential files provided with LAMMPS in the potentials
+directory are parameterized for real units.  You can use
 the ReaxFF potential with any LAMMPS units, but you would need to
 create your own potential file with coefficients listed in the
-appropriate units if your simulation doesn't use "real" units.  This
-would be somewhat tricky, so contact the LAMMPS authors if you wish to
-do this.
+appropriate units if your simulation doesn't use "real" units.
 

 
Related commands:
 

-
pair_coeff
+
pair_coeff, pair_style reax/c
 

 
Default: none
 

@@ -147,7 +157,7 @@ do this.
 
 
 
-
(Chenoweth) Chenoweth, van Duin and Goddard III, 
+
(Chenoweth) Chenoweth, van Duin and Goddard, 
 Journal of Physical Chemistry A, 112, 1040-1053 (2008).
 

 
diff --git a/doc/pair_reax.txt b/doc/pair_reax.txt
index e454f07ab1..9a16db174d 100644
--- a/doc/pair_reax.txt
+++ b/doc/pair_reax.txt
@@ -24,26 +24,38 @@ pair_coeff * * ffield.reax 3 NULL NULL 3 :pre
 
 [Description:]
 
-The pair style computes the ReaxFF potential of van Duin, Goddard and
+Style {reax} computes the ReaxFF potential of van Duin, Goddard and
 co-workers.  ReaxFF uses distance-dependent bond-order functions to
 represent the contributions of chemical bonding to the potential
-energy. There is more than one version of ReaxFF. The version implemented 
-in LAMMPS uses the functional forms documented in the
-supplemental information of the following paper: "(Chenoweth et al.,
- 2008)"_#Chenoweth_2008. 
+energy. There is more than one version of ReaxFF. The version
+implemented in LAMMPS uses the functional forms documented in the
+supplemental information of the following paper:
+"(Chenoweth)"_#Chenoweth.  The version integrated into LAMMPS matches
+the most up-to-date version of ReaxFF as of summer 2010.
 
-LAMMPS requires that a file called ffield.reax be provided, containing the
-ReaxFF parameters for each atom type, bond type, etc. The format is identical to
-the ffield file used by van Duin and co-workers. The filename is also
-reuqired as an argument in the pair_coeff command. Any value other than
-ffield.reax will be rejected (see below).
+The {reax} style differs from the "pair_style reax/c"_pair_reax_c.html
+command in the lo-level implementation details.  The {reax} style is a
+Fortran library, linked to LAMMPS.  The {reax/c} style was initially
+implemented as stand-alone C code and is now integrated into LAMMPS as
+a package.
 
-LAMMPS provides several different versions of ffield.reax
-in its potentials dir, each called potentials/ffield.reax.label.
-These are documented in potentials/README.reax.
-The default ffield.reax contains parameterizations for the following
-elements: C, H, O, N, S. You can use one of the other files in place of it, 
-or obtain a file from elsewhere.
+LAMMPS requires that a file called ffield.reax be provided, containing
+the ReaxFF parameters for each atom type, bond type, etc. The format
+is identical to the ffield file used by van Duin and co-workers. The
+filename is required as an argument in the pair_coeff command. Any
+value other than "ffield.reax" will be rejected (see below).
+
+LAMMPS provides several different versions of ffield.reax in its
+potentials dir, each called potentials/ffield.reax.label.  These are
+documented in potentials/README.reax.  The default ffield.reax
+contains parameterizations for the following elements: C, H, O, N, S.
+
+The format of these files is identical to that used originally by van
+Duin.  We have tested the accuracy of {pair_style reax/c} potential
+against the original ReaxFF code for the systems mentioned above.  You
+can use other ffield files for specific chemical systems that may be
+available elsewhere (but note that their accuracy may not have been
+tested).
 
 The {hbcut} and {precision} settings are optional arguments.  If
 neither is provided, default settings are used: {hbcut} = 10 (which is
@@ -52,9 +64,10 @@ If you wish to override either of these defaults, then both settings
 must be specified.
 
 Use of this pair style requires that a charge be defined for every
-atom since the potential performs charge equilibration.  See the
-"atom_style"_atom_style.html and "read_data"_read_data.html commands
-for details on how to specify charges.
+atom since the {reax} pair style performs a charge equilibration (QEq)
+calculation.  See the "atom_style"_atom_style.html and
+"read_data"_read_data.html commands for details on how to specify
+charges.
 
 The thermo variable {evdwl} stores the sum of all the ReaxFF potential
 energy contributions, with the exception of the Coulombic and charge
@@ -83,25 +96,24 @@ file into the directory you are running from.  If you wish to use
 another ReaxFF potential file, then name it "ffield.reax" and put it
 in the directory you run from.
 
-In the ReaxFF potential file, near the top, is a section that contains
-element names, each with a couple dozen numeric parameters.  The
-default ffield.reax provided with LAMMPS lists 5 elements: C, H, O, N,
-S.  Think of these as numbered 1 to 5.  When using this file each of
-the N indices you specify for the N atom types of LAMMPS atoms must be
-an integer from 1 to 5.  Atoms with LAMMPS type 1 will be mapped to
-whatever element you specify as the first index value, etc.  If a
-mapping value is specified as NULL, the mapping is not performed.
-This can be used when a ReaxFF potential is used as part of the
-{hybrid} pair style.  The NULL values are placeholders for atom types
-that will be used with other potentials.
+In the ReaxFF potential file, near the top, after the general
+parameters, is the atomic parameters section that contains element
+names, each with a couple dozen numeric parameters.  If there are M
+elements specified in the {ffield} file, think of these as numbered 1
+to M. Each of the N indices you specify for the N atom types of LAMMPS
+atoms must be an integer from 1 to M.  Atoms with LAMMPS type 1 will
+be mapped to whatever element you specify as the first index value,
+etc.  If a mapping value is specified as NULL, the mapping is not
+performed.  This can be used when a ReaxFF potential is used as part
+of the {hybrid} pair style.  The NULL values are placeholders for atom
+types that will be used with other potentials.
 
-In the pair_coeff example above with 3 1 2 2, the LAMMPS simulation
-has 4 atoms types and they are set as follows:
+As an example, say your LAMMPS simulation has 4 atom types and the
+elements are ordered as C, H, O, N in the {ffield} file.  If you want
+the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
+H, you would use the following pair_coeff command:
 
-type 1 = O
-type 2 = C
-type 3 = H
-type 4 = H :pre
+pair_coeff * * ffield.reax 1 1 4 2 :pre
 
 :line
 
@@ -126,23 +138,20 @@ LAMMPS was built with that package, which also requires the REAX
 library be built and linked with LAMMPS.  See the "Making
 LAMMPS"_Section_start.html#2_3 section for more info.
 
-The ffield.reax potential file provided with LAMMPS in the potentials
-directory is parameterized for real "units"_units.html.  You can use
+The ReaxFF potential files provided with LAMMPS in the potentials
+directory are parameterized for real "units"_units.html.  You can use
 the ReaxFF potential with any LAMMPS units, but you would need to
 create your own potential file with coefficients listed in the
-appropriate units if your simulation doesn't use "real" units.  This
-would be somewhat tricky, so contact the LAMMPS authors if you wish to
-do this.
+appropriate units if your simulation doesn't use "real" units.
 
 [Related commands:]
 
-"pair_coeff"_pair_coeff.html
+"pair_coeff"_pair_coeff.html, "pair_style reax/c"_pair_reax_c.html
 
 [Default:] none
 
 :line
 
 :link(Chenoweth_2008) 
-[(Chenoweth)] Chenoweth, van Duin and Goddard III, 
+[(Chenoweth)] Chenoweth, van Duin and Goddard, 
 Journal of Physical Chemistry A, 112, 1040-1053 (2008).
-