keyword = every or flush or format or image or precision or region or scale or sort or thresh or unwrap
element args = E1 E2 ... EN, where N = # of atom types
E1,...,EN = element name, e.g. C or Fe or Ga
@@ -31,6 +31,7 @@
precision arg = power-of-10 value from 10 to 1000000
region arg = region-ID or "none"
scale arg = yes or no
+ sort arg = yes or no
thresh args = attribute operation value
attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
operation = "<" or "<=" or ">" or ">=" or "==" or "!="
@@ -110,6 +111,12 @@
value of no means they are written in absolute distance units
(e.g. Angstroms or sigma).
+The sort keyword applies only to the dump cfg style. A sort value
+of yes means atoms will be written into the CFG file in sorted
+order, sorted by the atom ID. A value of no means a sort will not
+be performed and that atoms may be in an indeterminate order,
+depending on which processor owns which atoms.
+
The thresh keyword only applies to the dump custom and cfg
styles. Multiple thresholds can be specified. Specifying "none"
turns off all threshold criteria. If thresholds are specified, only
@@ -147,6 +154,7 @@
unwrap = no
diff -Naur lammps-2Sep09/doc/dump_modify.txt lammps-4Sep09/doc/dump_modify.txt
--- lammps-2Sep09/doc/dump_modify.txt 2009-09-02 10:20:52.000000000 -0600
+++ lammps-4Sep09/doc/dump_modify.txt 2009-09-02 14:56:46.000000000 -0600
@@ -14,7 +14,7 @@
dump-ID = ID of dump to modify :ulb,l
one or more keyword/value pairs may be appended :l
-keyword = {every} or {flush} or {format} or {image} or {precision} or {region} or {scale} or {thresh} or {unwrap} :l
+keyword = {every} or {flush} or {format} or {image} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
{element} args = E1 E2 ... EN, where N = # of atom types
E1,...,EN = element name, e.g. C or Fe or Ga
{every} arg = N
@@ -25,6 +25,7 @@
{precision} arg = power-of-10 value from 10 to 1000000
{region} arg = region-ID or "none"
{scale} arg = {yes} or {no}
+ {sort} arg = {yes} or {no}
{thresh} args = attribute operation value
attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
operation = "<" or "<=" or ">" or ">=" or "==" or "!="
@@ -103,6 +104,12 @@
value of {no} means they are written in absolute distance units
(e.g. Angstroms or sigma).
+The {sort} keyword applies only to the dump {cfg} style. A sort value
+of {yes} means atoms will be written into the CFG file in sorted
+order, sorted by the atom ID. A value of {no} means a sort will not
+be performed and that atoms may be in an indeterminate order,
+depending on which processor owns which atoms.
+
The {thresh} keyword only applies to the dump {custom} and {cfg}
styles. Multiple thresholds can be specified. Specifying "none"
turns off all threshold criteria. If thresholds are specified, only
@@ -140,5 +147,6 @@
precision = 1000
region = none
scale = yes
+sort = no
thresh = none
unwrap = no :ul
diff -Naur lammps-2Sep09/doc/fix_deform.html lammps-4Sep09/doc/fix_deform.html
--- lammps-2Sep09/doc/fix_deform.html 2009-04-28 08:56:27.000000000 -0600
+++ lammps-4Sep09/doc/fix_deform.html 2009-09-02 10:41:44.000000000 -0600
@@ -180,14 +180,16 @@
and delta is the change relative to the original length. Thus if the
trate R is 0.1 and time units are picoseconds, this means the box
length will increase by 10% of its current length every picosecond.
-I.e. strain after 1 psec = 0.1, strain after 2 psec = 0.21, etc.
-R = 1 or 2 means the box length will double or triple every
-picosecond. R = -0.01 means the box length will shrink by 1% of its
-current length every picosecond. Note that for a "true" rate the
-change is continuous and based on the current length, so running with
-R = 1 for 10 picoseconds does not expand the box length by a factor of
-10 as it would with erate, but by a factor of 1024 since it doubles
-every picosecond.
+I.e. strain after 1 psec = 0.1, strain after 2 psec = 0.21, etc. R =
+1 or 2 means the box length will double or triple every picosecond. R
+= -0.01 means the box length will shrink by 1% of its current length
+every picosecond. Note that for a "true" rate the change is
+continuous and based on the current length, so running with R = 1 for
+10 picoseconds does not expand the box length by a factor of 10 as it
+would with erate, but by a factor of 1024 since it doubles every
+picosecond. Note that the trate value must be greater than -1.0 to
+be valid, since a value of -1.0 would mean shrink the box size by 100%
+to a value of 0.0.
Note that to change the volume (or cross-sectional area) of the
simulation box at a constant rate, you can change multiple dimensions
@@ -302,8 +304,10 @@
by 1% every picosecond. Note that the change is continuous, so
running with R = 1 for 10 picoseconds does not change the tilt factor
by a factor of 10, but by a factor of 1024 since it doubles every
-picosecond. Also note that the initial tilt factor must be non-zero
-to use the trate option.
+picosecond. Note that the trate value must be greater than -1.0 to
+be valid, since a value of -1.0 would mean shrink the tilt by 100% to
+a value of 0.0. Also note that the initial tilt factor must be
+non-zero to use the trate option.
Note that shear strain is defined as the tilt factor divided by the
perpendicular box length. The erate and trate styles control the
diff -Naur lammps-2Sep09/doc/fix_deform.txt lammps-4Sep09/doc/fix_deform.txt
--- lammps-2Sep09/doc/fix_deform.txt 2009-04-28 08:56:27.000000000 -0600
+++ lammps-4Sep09/doc/fix_deform.txt 2009-09-02 10:41:44.000000000 -0600
@@ -170,14 +170,16 @@
and delta is the change relative to the original length. Thus if the
{trate} R is 0.1 and time units are picoseconds, this means the box
length will increase by 10% of its current length every picosecond.
-I.e. strain after 1 psec = 0.1, strain after 2 psec = 0.21, etc.
-R = 1 or 2 means the box length will double or triple every
-picosecond. R = -0.01 means the box length will shrink by 1% of its
-current length every picosecond. Note that for a "true" rate the
-change is continuous and based on the current length, so running with
-R = 1 for 10 picoseconds does not expand the box length by a factor of
-10 as it would with {erate}, but by a factor of 1024 since it doubles
-every picosecond.
+I.e. strain after 1 psec = 0.1, strain after 2 psec = 0.21, etc. R =
+1 or 2 means the box length will double or triple every picosecond. R
+= -0.01 means the box length will shrink by 1% of its current length
+every picosecond. Note that for a "true" rate the change is
+continuous and based on the current length, so running with R = 1 for
+10 picoseconds does not expand the box length by a factor of 10 as it
+would with {erate}, but by a factor of 1024 since it doubles every
+picosecond. Note that the {trate} value must be greater than -1.0 to
+be valid, since a value of -1.0 would mean shrink the box size by 100%
+to a value of 0.0.
Note that to change the volume (or cross-sectional area) of the
simulation box at a constant rate, you can change multiple dimensions
@@ -292,8 +294,10 @@
by 1% every picosecond. Note that the change is continuous, so
running with R = 1 for 10 picoseconds does not change the tilt factor
by a factor of 10, but by a factor of 1024 since it doubles every
-picosecond. Also note that the initial tilt factor must be non-zero
-to use the {trate} option.
+picosecond. Note that the {trate} value must be greater than -1.0 to
+be valid, since a value of -1.0 would mean shrink the tilt by 100% to
+a value of 0.0. Also note that the initial tilt factor must be
+non-zero to use the {trate} option.
Note that shear strain is defined as the tilt factor divided by the
perpendicular box length. The {erate} and {trate} styles control the
diff -Naur lammps-2Sep09/lib/gpu/gb_gpu.cu lammps-4Sep09/lib/gpu/gb_gpu.cu
--- lammps-2Sep09/lib/gpu/gb_gpu.cu 2009-08-13 10:05:41.000000000 -0600
+++ lammps-4Sep09/lib/gpu/gb_gpu.cu 2009-09-04 09:03:44.000000000 -0600
@@ -116,6 +116,7 @@
form[ii]=_form_(itype,jtype);
}
ii+=INT_MUL(blockIdx.x,blockDim.x)+start;
+ __syncthreads();
if (iisfree(params);
params = NULL;
- nparams = 0;
+ nparams = maxparam = 0;
// open file on proc 0
diff -Naur lammps-2Sep09/src/fix_deform.cpp lammps-4Sep09/src/fix_deform.cpp
--- lammps-2Sep09/src/fix_deform.cpp 2009-08-18 12:11:26.000000000 -0600
+++ lammps-4Sep09/src/fix_deform.cpp 2009-09-02 10:38:58.000000000 -0600
@@ -103,6 +103,8 @@
if (iarg+3 > narg) error->all("Illegal fix deform command");
set[index].style = TRATE;
set[index].rate = atof(arg[iarg+2]);
+ if (set[index].rate <= -1.0)
+ error->all("Fix deform trate must be > -1.0");
iarg += 3;
} else if (strcmp(arg[iarg+1],"volume") == 0) {
set[index].style = VOLUME;
@@ -152,6 +154,8 @@
if (iarg+3 > narg) error->all("Illegal fix deform command");
set[index].style = TRATE;
set[index].rate = atof(arg[iarg+2]);
+ if (set[index].rate <= -1.0)
+ error->all("Fix deform trate must be > -1.0");
iarg += 3;
} else if (strcmp(arg[iarg+1],"wiggle") == 0) {
if (iarg+4 > narg) error->all("Illegal fix deform command");
diff -Naur lammps-2Sep09/tools/ch2lmp/lammps2pdb.pl lammps-4Sep09/tools/ch2lmp/lammps2pdb.pl
--- lammps-2Sep09/tools/ch2lmp/lammps2pdb.pl 2007-10-05 11:27:10.000000000 -0600
+++ lammps-4Sep09/tools/ch2lmp/lammps2pdb.pl 2009-09-04 09:02:22.000000000 -0600
@@ -776,7 +776,8 @@
my $subject = "item: ".lc(shift(@_));
my $advance = 1;
- while (!eof(TRAJECT)&&(lc(join(" ", split(" ", ))) ne $subject)) {}
+ while (!eof(TRAJECT)&&(substr(lc(join(" ", split(" ", ))),
+ 0,length($subject)) ne $subject)) {}
}