git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1385 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_modify.html

@@ -501,7 +501,7 @@ other variables = v_a, v_myvar, ...
 math functions = div(x,y), mult(x,y), add(x,y), ...
 group functions = mass(group), xcm(group,x), ...
 atom values = x<B>123</B>, y<B>3</B>, vx<B>34</B>, ...
-compute values = c_mytemp<B>0</B>, c_thermo_pressure<B>3</B>, ...
+compute values = c_mytemp<B>0</B>, c_thermo_press<B>3</B>, ...
 </P>
 <P>Adding keywords for the <A HREF = "themo_style.html">thermo_style custom</A> command
 (which can then be accessed by variables) was discussed

doc/Section_modify.txt

@@ -478,7 +478,7 @@ other variables = v_a, v_myvar, ...
 math functions = div(x,y), mult(x,y), add(x,y), ...
 group functions = mass(group), xcm(group,x), ...
 atom values = x[123], y[3], vx[34], ...
-compute values = c_mytemp[0], c_thermo_pressure[3], ...
+compute values = c_mytemp[0], c_thermo_press[3], ...
 
 Adding keywords for the "thermo_style custom"_themo_style.html command
 (which can then be accessed by variables) was discussed

doc/Section_start.html

@@ -186,15 +186,15 @@ the KSPACE package (see below).
 </P>
 <P>(7) There are a few other -D compiler switches you can set as part of
 CCFLAGS.  The read_data and dump commands will read/write gzipped
-files if you compile with -DGZIP.  It requires that your Unix support
-the "popen" command.  Using one of the -DPACK_ARRAY, -DPACK_POINTER,
-and -DPACK_MEMCPY options can make for faster parallel FFTs (in the
-PPPM solver) on some platforms.  The -DPACK_ARRAY setting is the
-default.  If you compile with -DLAMMPS_XDR, the build will include XDR
-compatability files for doing particle dumps in XTC format.  This is
-only necessary if your platform does have its own XDR files available.
-See the Restrictions section of the <A HREF = "dump.html">dump</A> command for
-details.
+files if you compile with -DLAMMPS_GZIP.  It requires that your Unix
+support the "popen" command.  Using one of the -DPACK_ARRAY,
+-DPACK_POINTER, and -DPACK_MEMCPY options can make for faster parallel
+FFTs (in the PPPM solver) on some platforms.  The -DPACK_ARRAY setting
+is the default.  If you compile with -DLAMMPS_XDR, the build will
+include XDR compatability files for doing particle dumps in XTC
+format.  This is only necessary if your platform does have its own XDR
+files available.  See the Restrictions section of the <A HREF = "dump.html">dump</A>
+command for details.
 </P>
 <P>(8) The DEPFLAGS setting is how the C++ compiler creates a dependency
 file for each source file.  This speeds re-compilation when source

doc/Section_start.txt

@@ -181,15 +181,15 @@ the KSPACE package (see below).
 
 (7) There are a few other -D compiler switches you can set as part of
 CCFLAGS.  The read_data and dump commands will read/write gzipped
-files if you compile with -DGZIP.  It requires that your Unix support
-the "popen" command.  Using one of the -DPACK_ARRAY, -DPACK_POINTER,
-and -DPACK_MEMCPY options can make for faster parallel FFTs (in the
-PPPM solver) on some platforms.  The -DPACK_ARRAY setting is the
-default.  If you compile with -DLAMMPS_XDR, the build will include XDR
-compatability files for doing particle dumps in XTC format.  This is
-only necessary if your platform does have its own XDR files available.
-See the Restrictions section of the "dump"_dump.html command for
-details.
+files if you compile with -DLAMMPS_GZIP.  It requires that your Unix
+support the "popen" command.  Using one of the -DPACK_ARRAY,
+-DPACK_POINTER, and -DPACK_MEMCPY options can make for faster parallel
+FFTs (in the PPPM solver) on some platforms.  The -DPACK_ARRAY setting
+is the default.  If you compile with -DLAMMPS_XDR, the build will
+include XDR compatability files for doing particle dumps in XTC
+format.  This is only necessary if your platform does have its own XDR
+files available.  See the Restrictions section of the "dump"_dump.html
+command for details.
 
 (8) The DEPFLAGS setting is how the C++ compiler creates a dependency
 file for each source file.  This speeds re-compilation when source

doc/compute.html

@@ -76,11 +76,11 @@ computes for further info.
 </P>
 <P>LAMMPS creates its own global computes for thermodynamic output.
 Three computes are always created, named "thermo_temp",
-"thermo_pressure", and "thermo_pe", as if these commands had been
-invoked in the input script:
+"thermo_press", and "thermo_pe", as if these commands had been invoked
+in the input script:
 </P>
 <PRE>compute thermo_temp all temp
-compute thermo_pressure all pressure thermo_temp
+compute thermo_press all pressure thermo_temp
 compute thermo_pe all pe 
 </PRE>
 <P>Additional computes for other quantities are created if the thermo

doc/compute.txt

@@ -73,11 +73,11 @@ computes for further info.
 
 LAMMPS creates its own global computes for thermodynamic output.
 Three computes are always created, named "thermo_temp",
-"thermo_pressure", and "thermo_pe", as if these commands had been
-invoked in the input script:
+"thermo_press", and "thermo_pe", as if these commands had been invoked
+in the input script:
 
 compute thermo_temp all temp
-compute thermo_pressure all pressure thermo_temp
+compute thermo_press all pressure thermo_temp
 compute thermo_pe all pe :pre
 
 Additional computes for other quantities are created if the thermo

doc/compute_pressure.html

@@ -74,10 +74,10 @@ atoms or other degrees of freedom.
 where the DOF is specified by the temperature compute.  See the
 various <A HREF = "compute.html">compute temperature</A> styles for details.
 </P>
-<P>A compute of this style with the ID of "thermo_pressure" is created
-when LAMMPS starts up, as if this command were in the input script:
+<P>A compute of this style with the ID of "thermo_press" is created when
+LAMMPS starts up, as if this command were in the input script:
 </P>
-<PRE>compute thermo_pressure all pressure thermo_temp 
+<PRE>compute thermo_press all pressure thermo_temp 
 </PRE>
 <P>where "thermo_temp" is the ID of a similarly defined compute of style
 "temp".  See the "thermo_style" command for more details.

doc/compute_pressure.txt

@@ -71,10 +71,10 @@ Note that the N is the above formula is really degrees-of-freedom
 where the DOF is specified by the temperature compute.  See the
 various "compute temperature"_compute.html styles for details.
 
-A compute of this style with the ID of "thermo_pressure" is created
-when LAMMPS starts up, as if this command were in the input script:
+A compute of this style with the ID of "thermo_press" is created when
+LAMMPS starts up, as if this command were in the input script:
 
-compute thermo_pressure all pressure thermo_temp :pre
+compute thermo_press all pressure thermo_temp :pre
 
 where "thermo_temp" is the ID of a similarly defined compute of style
 "temp".  See the "thermo_style" command for more details.

doc/dump.html

@@ -309,9 +309,9 @@ used to change it.  The exception is DCD files which store the tilt
 factors for subsequent visualization by programs like
 <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>.
 </P>
-<P>To write gzipped dump files, you must compile LAMMPS with the -DGZIP
-option - see the <A HREF = "Section_start.html#2_2">Making LAMMPS</A> section of the
-documentation.
+<P>To write gzipped dump files, you must compile LAMMPS with the
+-DLAMMPS_GZIP option - see the <A HREF = "Section_start.html#2_2">Making LAMMPS</A>
+section of the documentation.
 </P>
 <P>The <I>bond</I> style is part of the "molecular" package.  It is only
 enabled if LAMMPS was built with that package.  See the <A HREF = "Section_start.html#2_3">Making

doc/dump.txt

@@ -299,9 +299,9 @@ used to change it.  The exception is DCD files which store the tilt
 factors for subsequent visualization by programs like
 "VMD"_http://www.ks.uiuc.edu/Research/vmd.
 
-To write gzipped dump files, you must compile LAMMPS with the -DGZIP
-option - see the "Making LAMMPS"_Section_start.html#2_2 section of the
-documentation.
+To write gzipped dump files, you must compile LAMMPS with the
+-DLAMMPS_GZIP option - see the "Making LAMMPS"_Section_start.html#2_2
+section of the documentation.
 
 The {bond} style is part of the "molecular" package.  It is only
 enabled if LAMMPS was built with that package.  See the "Making

doc/fix_ave_time.html

@@ -51,7 +51,7 @@
 <P><B>Examples:</B>
 </P>
 <PRE>fix 1 all ave/time 100 5 1000 myTemp thermo_temp file temp.profile
-fix 1 all ave/time 100 5 1000 thermo_pressure<B>2</B> ave window 20
+fix 1 all ave/time 100 5 1000 thermo_press<B>2</B> ave window 20
 fix 1 all ave/time 1 100 1000 f_indent f_indent<B>1</B> file temp.indent 
 </PRE>
 <P><B>Description:</B>

doc/fix_ave_time.txt

@@ -38,7 +38,7 @@ keyword = {file} or {ave} :l
 [Examples:]
 
 fix 1 all ave/time 100 5 1000 myTemp thermo_temp file temp.profile
-fix 1 all ave/time 100 5 1000 thermo_pressure[2] ave window 20
+fix 1 all ave/time 100 5 1000 thermo_press[2] ave window 20
 fix 1 all ave/time 1 100 1000 f_indent f_indent[1] file temp.indent :pre
 
 [Description:]

doc/fix_nph.html

@@ -139,13 +139,13 @@ as the fix group.
 </P>
 <P>Note that these are NOT the computes used by thermodynamic output (see
 the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
-and <I>thermo_pressure</I>.  This means you can change the attributes of
-this fix's temperature or pressure via the
+and <I>thermo_press</I>.  This means you can change the attributes of this
+fix's temperature or pressure via the
 <A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
 or pressure during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
 custom</A> command using the appropriate compute-ID.
 It also means that changing attributes of <I>thermo_temp</I> or
-<I>thermo_pressure</I> will have no effect on this fix.
+<I>thermo_press</I> will have no effect on this fix.
 </P>
 <P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
 </P>

doc/fix_nph.txt

@@ -129,13 +129,13 @@ as the fix group.
 
 Note that these are NOT the computes used by thermodynamic output (see
 the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
-and {thermo_pressure}.  This means you can change the attributes of
-this fix's temperature or pressure via the
+and {thermo_press}.  This means you can change the attributes of this
+fix's temperature or pressure via the
 "compute_modify"_compute_modify.html command or print this temperature
 or pressure during thermodyanmic output via the "thermo_style
 custom"_thermo_style.html command using the appropriate compute-ID.
 It also means that changing attributes of {thermo_temp} or
-{thermo_pressure} will have no effect on this fix.
+{thermo_press} will have no effect on this fix.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 

doc/fix_npt.html

@@ -143,13 +143,13 @@ as the fix group.
 </P>
 <P>Note that these are NOT the computes used by thermodynamic output (see
 the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
-and <I>thermo_pressure</I>.  This means you can change the attributes of
-this fix's temperature or pressure via the
+and <I>thermo_press</I>.  This means you can change the attributes of this
+fix's temperature or pressure via the
 <A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
 or pressure during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
 custom</A> command using the appropriate compute-ID.
 It also means that changing attributes of <I>thermo_temp</I> or
-<I>thermo_pressure</I> will have no effect on this fix.
+<I>thermo_press</I> will have no effect on this fix.
 </P>
 <P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
 </P>

doc/fix_npt.txt

@@ -132,13 +132,13 @@ as the fix group.
 
 Note that these are NOT the computes used by thermodynamic output (see
 the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
-and {thermo_pressure}.  This means you can change the attributes of
-this fix's temperature or pressure via the
+and {thermo_press}.  This means you can change the attributes of this
+fix's temperature or pressure via the
 "compute_modify"_compute_modify.html command or print this temperature
 or pressure during thermodyanmic output via the "thermo_style
 custom"_thermo_style.html command using the appropriate compute-ID.
 It also means that changing attributes of {thermo_temp} or
-{thermo_pressure} will have no effect on this fix.
+{thermo_press} will have no effect on this fix.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 

doc/fix_npt_asphere.html

@@ -142,13 +142,13 @@ as the fix group.
 </P>
 <P>Note that these are NOT the computes used by thermodynamic output (see
 the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
-and <I>thermo_pressure</I>.  This means you can change the attributes of
-this fix's temperature or pressure via the
+and <I>thermo_press</I>.  This means you can change the attributes of this
+fix's temperature or pressure via the
 <A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
 or pressure during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
 custom</A> command using the appropriate compute-ID.
 It also means that changing attributes of <I>thermo_temp</I> or
-<I>thermo_pressure</I> will have no effect on this fix.
+<I>thermo_press</I> will have no effect on this fix.
 </P>
 <P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
 </P>

doc/fix_npt_asphere.txt

@@ -131,13 +131,13 @@ as the fix group.
 
 Note that these are NOT the computes used by thermodynamic output (see
 the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
-and {thermo_pressure}.  This means you can change the attributes of
-this fix's temperature or pressure via the
+and {thermo_press}.  This means you can change the attributes of this
+fix's temperature or pressure via the
 "compute_modify"_compute_modify.html command or print this temperature
 or pressure during thermodyanmic output via the "thermo_style
 custom"_thermo_style.html command using the appropriate compute-ID.
 It also means that changing attributes of {thermo_temp} or
-{thermo_pressure} will have no effect on this fix.
+{thermo_press} will have no effect on this fix.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 

doc/fix_tmd.html

@@ -41,7 +41,8 @@ group and the target coordinates listed in file1.  Thus a value of
 rho_final = 0.0 means move the atoms all the way to the final
 structure during the course of the run.
 </P>
-<P>The format of the target file1 is as follows:
+<P>The target file1 can be ASCII text or a gzipped text file (detected by
+a .gz suffix).  The format of the target file1 is as follows:
 </P>
 <PRE>0.0 25.0 xlo xhi
 0.0 25.0 ylo yhi
@@ -112,6 +113,10 @@ which a SHAKE fix is applied.  This is because LAMMPS assumes there
 are not multiple competing holonomic constraints applied to the same
 atoms.
 </P>
+<P>To read gzipped target files, you must compile LAMMPS with the
+-DLAMMPS_GZIP option - see the <A HREF = "Section_start.html#2_2">Making LAMMPS</A>
+section of the documentation.
+</P>
 <P><B>Related commands:</B> none
 </P>
 <P><B>Default:</B> none

doc/fix_tmd.txt

@@ -38,7 +38,8 @@ group and the target coordinates listed in file1.  Thus a value of
 rho_final = 0.0 means move the atoms all the way to the final
 structure during the course of the run.
 
-The format of the target file1 is as follows:
+The target file1 can be ASCII text or a gzipped text file (detected by
+a .gz suffix).  The format of the target file1 is as follows:
 
 0.0 25.0 xlo xhi
 0.0 25.0 ylo yhi
@@ -109,6 +110,10 @@ which a SHAKE fix is applied.  This is because LAMMPS assumes there
 are not multiple competing holonomic constraints applied to the same
 atoms.
 
+To read gzipped target files, you must compile LAMMPS with the
+-DLAMMPS_GZIP option - see the "Making LAMMPS"_Section_start.html#2_2
+section of the documentation.
+
 [Related commands:] none
 
 [Default:] none

doc/read_data.html

@@ -684,9 +684,9 @@ units of angular velocity (radians/time).
 
 <P><B>Restrictions:</B>
 </P>
-<P>To read gzipped data files, you must compile LAMMPS with the -DGZIP
-option - see the <A HREF = "Section_start.html#2_2">Making LAMMPS</A> section of the
-documentation.
+<P>To read gzipped data files, you must compile LAMMPS with the
+-DLAMMPS_GZIP option - see the <A HREF = "Section_start.html#2_2">Making LAMMPS</A>
+section of the documentation.
 </P>
 <P><B>Related commands:</B>
 </P>

doc/read_data.txt

@@ -594,9 +594,9 @@ Translational velocities can also be set by the
 
 [Restrictions:]
 
-To read gzipped data files, you must compile LAMMPS with the -DGZIP
-option - see the "Making LAMMPS"_Section_start.html#2_2 section of the
-documentation.
+To read gzipped data files, you must compile LAMMPS with the
+-DLAMMPS_GZIP option - see the "Making LAMMPS"_Section_start.html#2_2
+section of the documentation.
 
 [Related commands:]
 

doc/thermo_modify.html

@@ -99,8 +99,8 @@ compute ID must have been previously defined by the user via the
 <A HREF = "compute.html">compute</A> command and it must be a style of compute that
 calculates a pressure.  As described in the
 <A HREF = "thermo_style.html">thermo_style</A> command, thermo output uses a default
-compute for pressure with ID = <I>thermo_pressure</I>.  This option allows
-the user to override the default.
+compute for pressure with ID = <I>thermo_press</I>.  This option allows the
+user to override the default.
 </P>
 <P>The <I>drot</I> keyword is used to determine how rotational energy is
 calculated for dipolar atoms, which is used by the thermo_style

doc/thermo_modify.txt

@@ -93,8 +93,8 @@ compute ID must have been previously defined by the user via the
 "compute"_compute.html command and it must be a style of compute that
 calculates a pressure.  As described in the
 "thermo_style"_thermo_style.html command, thermo output uses a default
-compute for pressure with ID = {thermo_pressure}.  This option allows
-the user to override the default.
+compute for pressure with ID = {thermo_press}.  This option allows the
+user to override the default.
 
 The {drot} keyword is used to determine how rotational energy is
 calculated for dipolar atoms, which is used by the thermo_style

doc/thermo_style.html

@@ -139,13 +139,13 @@ This is done via the <A HREF = "thermo_modify.html">thermo_modify</A> command.
 </P>
 <P>Several of the thermodynamic quantities require a pressure to be
 computed: "press", "enthalpy", "pxx", etc.  By default this is done by
-using the "thermo_pressure" compute which is created when LAMMPS
-starts up, as if this command had been issued:
+using the pressure compute which is created when LAMMPS starts up, as
+if this command had been issued:
 </P>
-<PRE>compute thermo_pressure all pressure thermo_temp 
+<PRE>compute thermo_press all pressure thermo_temp 
 </PRE>
 <P>See the <A HREF = "compute_pressure.html">compute pressure</A> command for details.
-Note that the ID of this compute is <I>thermo_pressure</I> and the group is
+Note that the ID of this compute is <I>thermo_press</I> and the group is
 <I>all</I>.  You can change the attributes of this pressure via the
 <A HREF = "compute_modify.html">compute_modify</A> command.  Alternatively, you can
 directly assign a new compute (that calculates pressure) which you

doc/thermo_style.txt

@@ -133,13 +133,13 @@ This is done via the "thermo_modify"_thermo_modify.html command.
 
 Several of the thermodynamic quantities require a pressure to be
 computed: "press", "enthalpy", "pxx", etc.  By default this is done by
-using the "thermo_pressure" compute which is created when LAMMPS
-starts up, as if this command had been issued:
+using the pressure compute which is created when LAMMPS starts up, as
+if this command had been issued:
 
-compute thermo_pressure all pressure thermo_temp :pre
+compute thermo_press all pressure thermo_temp :pre
 
 See the "compute pressure"_compute_pressure.html command for details.
-Note that the ID of this compute is {thermo_pressure} and the group is
+Note that the ID of this compute is {thermo_press} and the group is
 {all}.  You can change the attributes of this pressure via the
 "compute_modify"_compute_modify.html command.  Alternatively, you can
 directly assign a new compute (that calculates pressure) which you