From 8b031ab609336956d59aaa8ff2b54ffac7a7d009 Mon Sep 17 00:00:00 2001
From: sjplimp
Date: Thu, 27 Jun 2013 14:21:12 +0000
Subject: [PATCH 01/38] git-svn-id:
svn://svn.icms.temple.edu/lammps-ro/trunk@10099
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
lib/meam/Makefile.gfortran | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/lib/meam/Makefile.gfortran b/lib/meam/Makefile.gfortran
index a1a829ef75..fe7de2200d 100644
--- a/lib/meam/Makefile.gfortran
+++ b/lib/meam/Makefile.gfortran
@@ -11,7 +11,7 @@ SHELL = /bin/sh
# which file will be copied to Makefile.lammps
-EXTRAMAKE = Makefile.lammps.installed
+EXTRAMAKE = Makefile.lammps.gfortran
# ------ FILES ------
From 33e5f0e99ad0484347304c502d928ef4bd87ea44 Mon Sep 17 00:00:00 2001
From: sjplimp
Date: Thu, 27 Jun 2013 19:43:07 +0000
Subject: [PATCH 02/38] git-svn-id:
svn://svn.icms.temple.edu/lammps-ro/trunk@10100
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
doc/Section_howto.html | 11 +++++++++++
doc/Section_howto.txt | 11 +++++++++++
doc/thermo_style.html | 8 ++++----
doc/thermo_style.txt | 8 ++++----
4 files changed, 30 insertions(+), 8 deletions(-)
diff --git a/doc/Section_howto.html b/doc/Section_howto.html
index 7d8677f8e2..3b63c4fa43 100644
--- a/doc/Section_howto.html
+++ b/doc/Section_howto.html
@@ -1359,6 +1359,17 @@ output. In each case, the compute, fix, or variable must generate
global values for input to the thermo_style custom
command.
+Note that thermodynamic output values can be "extensive" or
+"intensive". The former scale with the number of atoms in the system
+(e.g. total energy), the latter do not (e.g. temperature). The
+setting for thermo_modify norm determines whether
+extensive quantities are normalized or not. Computes and fixes
+produce either extensive or intensive values; see their individual doc
+pages for details. Equal-style variables produce only
+intensive values; you can include a division by "natoms" in the
+formula if desired, to make an extensive calculation produce an
+intensive result.
+
Dump file output
Dump file output is specified by the dump and
diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt
index f8254f90b9..49ad45fbda 100644
--- a/doc/Section_howto.txt
+++ b/doc/Section_howto.txt
@@ -1348,6 +1348,17 @@ output. In each case, the compute, fix, or variable must generate
global values for input to the "thermo_style custom"_dump.html
command.
+Note that thermodynamic output values can be "extensive" or
+"intensive". The former scale with the number of atoms in the system
+(e.g. total energy), the latter do not (e.g. temperature). The
+setting for "thermo_modify norm"_thermo_modify.html determines whether
+extensive quantities are normalized or not. Computes and fixes
+produce either extensive or intensive values; see their individual doc
+pages for details. "Equal-style variables"_variable.html produce only
+intensive values; you can include a division by "natoms" in the
+formula if desired, to make an extensive calculation produce an
+intensive result.
+
Dump file output :h5,link(dump)
Dump file output is specified by the "dump"_dump.html and
diff --git a/doc/thermo_style.html b/doc/thermo_style.html
index 78bcc3038e..fe94a4d8d5 100644
--- a/doc/thermo_style.html
+++ b/doc/thermo_style.html
@@ -308,10 +308,10 @@ equal-style variables can be referenced. See the
or they can invoke other computes, fixes, or variables when evaluated,
so this is a very general means of creating thermodynamic output.
-See Section_modify for information on how to add
-new compute and fix styles to LAMMPS to calculate quantities that can
-then be referenced with these keywords to generate thermodynamic
-output.
+
Note that equal-style variables are assumed to be "intensive" global
+quantities, which are thus printed as-is, without normalization by
+thermo_style custom. You can include a division by "natoms" in the
+variable formula if this is not the case.
diff --git a/doc/thermo_style.txt b/doc/thermo_style.txt
index 29acefe6ab..a4f06ed840 100644
--- a/doc/thermo_style.txt
+++ b/doc/thermo_style.txt
@@ -302,10 +302,10 @@ equal-style variables can be referenced. See the
or they can invoke other computes, fixes, or variables when evaluated,
so this is a very general means of creating thermodynamic output.
-See "Section_modify"_Section_modify.html for information on how to add
-new compute and fix styles to LAMMPS to calculate quantities that can
-then be referenced with these keywords to generate thermodynamic
-output.
+Note that equal-style variables are assumed to be "intensive" global
+quantities, which are thus printed as-is, without normalization by
+thermo_style custom. You can include a division by "natoms" in the
+variable formula if this is not the case.
:line
From e0211874ac3cdbc545fa0477085aee113b8a972b Mon Sep 17 00:00:00 2001
From: sjplimp
Date: Thu, 27 Jun 2013 19:49:41 +0000
Subject: [PATCH 03/38] git-svn-id:
svn://svn.icms.temple.edu/lammps-ro/trunk@10101
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/USER-MISC/pair_list.cpp | 3 +++
src/USER-MISC/pair_list.h | 38 +++++++++++++++++++++++++++++++++++++
src/atom.h | 6 ++++--
3 files changed, 45 insertions(+), 2 deletions(-)
diff --git a/src/USER-MISC/pair_list.cpp b/src/USER-MISC/pair_list.cpp
index d1e2e93ce1..d23215a9b9 100644
--- a/src/USER-MISC/pair_list.cpp
+++ b/src/USER-MISC/pair_list.cpp
@@ -375,6 +375,9 @@ void PairList::init_style()
if (atom->tag_enable == 0)
error->all(FLERR,"Pair style list requires atom IDs");
+ if (atom->map_style == 0)
+ error->all(FLERR,"Pair style list requires an atom map");
+
if (offset_flag) {
for (int n=0; n < npairs; ++n) {
list_parm_t &par = params[n];
diff --git a/src/USER-MISC/pair_list.h b/src/USER-MISC/pair_list.h
index 8869a52f52..9d199f5ba7 100644
--- a/src/USER-MISC/pair_list.h
+++ b/src/USER-MISC/pair_list.h
@@ -74,5 +74,43 @@ class PairList : public Pair {
/* ERROR/WARNING messages:
+E: Not all pairs processed in pair_style list
+
+Not all interacting pairs for which coefficients were found. This can be intentional
+and then you need to set the 'nocheck' option. If not, it usually means that the
+communication cutoff is too small. This can be ameliorated by either increasing
+the cutoff in the pair_style command or the communication cutoff.
+
+E: Illegal ... command
+
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Cannot open pair list file
+
+Self-explanatory. The file with the list of pairs cannot be open for reading.
+Check the path and permissions.
+
+E: Incorrectly formatted ...
+
+Self-explanatory. The content of the pair list file does not match the documented
+format. Please re-read the documentation and carefully compare it to your file.
+
+E: Unknown pair list potential style
+
+Self-explanatory. You requested a potential type that is not yet implemented or have a typo.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory. Check the input script or data file.
+
+E: Pair style list requires atom IDs
+
+Self-explanatory. The pairs in the list are identified via atom IDs, so they need to be present.
+
+E: Pair style list requires an atom map
+
+Self-explanatory. Atoms are looked up via an atom map. Create one using the atom_style map command.
*/
diff --git a/src/atom.h b/src/atom.h
index 375417942f..4d617585ae 100644
--- a/src/atom.h
+++ b/src/atom.h
@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
@@ -185,10 +185,12 @@ class Atom : protected Pointers {
// functions for global to local ID mapping
// map lookup function inlined for efficiency
+ // return -1 if no map defined
inline int map(int global) {
if (map_style == 1) return map_array[global];
- else return map_find_hash(global);
+ else if (map_style == 2) return map_find_hash(global);
+ else return -1;
};
void map_init();
From 0d6f0c69fd62079c1a653b5472e6e63d2619b59b Mon Sep 17 00:00:00 2001
From: sjplimp
Date: Thu, 27 Jun 2013 19:57:07 +0000
Subject: [PATCH 04/38] git-svn-id:
svn://svn.icms.temple.edu/lammps-ro/trunk@10102
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
doc/pair_sph_taitwater_morris.html | 2 +-
doc/pair_sph_taitwater_morris.txt | 2 +-
doc/pair_tersoff_zbl.html | 2 +-
doc/pair_tersoff_zbl.txt | 2 +-
doc/tad.html | 2 +-
doc/tad.txt | 2 +-
6 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/doc/pair_sph_taitwater_morris.html b/doc/pair_sph_taitwater_morris.html
index 4abffb4c53..4a2568ff79 100644
--- a/doc/pair_sph_taitwater_morris.html
+++ b/doc/pair_sph_taitwater_morris.html
@@ -78,6 +78,6 @@ LAMMPS section for more info.
-(Morris) Morris, Fox, Zhu, J Comp Physics, 136, 214–226 (1997).
+
(Morris) Morris, Fox, Zhu, J Comp Physics, 136, 214-226 (1997).