Commit b63b44e2 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5200 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 88e05949

doc/Manual.html

+39 −5
Original line number Diff line number Diff line
@@ -157,6 +157,8 @@ listed above. 
  4.17 <A HREF = "Section_howto.html#4_17">Walls</A> 

<BR>

  4.18 <A HREF = "Section_howto.html#4_18">Elastic constants</A> 

<BR>

  4.19 <A HREF = "Section_howto.html#4_19">Library interface to LAMMPS</A> 

<BR></UL>

<LI><A HREF = "Section_example.html">Example problems</A>
@@ -166,19 +168,35 @@ listed above. 


<LI><A HREF = "Section_modify.html">Modifying & Extending LAMMPS</A> 



<LI><A HREF = "Section_python.html">Python interface</A> 



<UL>  9.1 <A HREF = "Section_python.html#9_1">Extending Python with a serial version of LAMMPS</A> 

<BR>

  9.2 <A HREF = "Section_python.html#9_2">Creating a shared MPI library</A> 

<BR>

  9.3 <A HREF = "Section_python.html#9_3">Extending Python with a parallel version of LAMMPS</A> 

<BR>

  9.4 <A HREF = "Section_python.html#9_4">Extending Python with MPI</A> 

<BR>

  9.5 <A HREF = "Section_python.html#9_5">Testing the Python-LAMMPS interface</A> 

<BR>

  9.6 <A HREF = "Section_python.html#9_6">Using LAMMPS from Python</A> 

<BR>

  9.7 <A HREF = "Section_python.html#9_7">Example Python scripts that use LAMMPS</A> 

<BR></UL>

<LI><A HREF = "Section_errors.html">Errors</A> 



<UL>  9.1 <A HREF = "Section_errors.html#9_1">Common problems</A> 

<UL>  10.1 <A HREF = "Section_errors.html#10_1">Common problems</A> 

<BR>

  9.2 <A HREF = "Section_errors.html#9_2">Reporting bugs</A> 

  10.2 <A HREF = "Section_errors.html#10_2">Reporting bugs</A> 

<BR>

  9.3 <A HREF = "Section_errors.html#9_3">Error & warning messages</A> 

  10.3 <A HREF = "Section_errors.html#10_3">Error & warning messages</A> 

<BR></UL>

<LI><A HREF = "Section_history.html">Future and history</A> 



<UL>  10.1 <A HREF = "Section_history.html#10_1">Coming attractions</A> 

<UL>  11.1 <A HREF = "Section_history.html#11_1">Coming attractions</A> 

<BR>

  10.2 <A HREF = "Section_history.html#10_2">Past versions</A> 

  11.2 <A HREF = "Section_history.html#11_2">Past versions</A> 

<BR></UL>



</OL>
@@ -249,6 +267,22 @@ listed above.

doc/Manual.txt

+31 −13
Original line number Diff line number Diff line
@@ -112,18 +112,27 @@ listed above. 
  4.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_4_15 :b

  4.16 "Thermostatting, barostatting, and compute temperature"_4_16 :b

  4.17 "Walls"_4_17 :b

  4.18 "Elastic constants"_4_18 :ule,b

  4.18 "Elastic constants"_4_18 :b

  4.19 "Library interface to LAMMPS"_4_19 :ule,b

"Example problems"_Section_example.html :l

"Performance & scalability"_Section_perf.html :l

"Additional tools"_Section_tools.html :l

"Modifying & Extending LAMMPS"_Section_modify.html :l

"Python interface"_Section_python.html :l

  9.1 "Extending Python with a serial version of LAMMPS"_9_1 :ulb,b

  9.2 "Creating a shared MPI library"_9_2 :b

  9.3 "Extending Python with a parallel version of LAMMPS"_9_3 :b

  9.4 "Extending Python with MPI"_9_4 :b

  9.5 "Testing the Python-LAMMPS interface"_9_5 :b

  9.6 "Using LAMMPS from Python"_9_6 :b

  9.7 "Example Python scripts that use LAMMPS"_9_7 :ule,b

"Errors"_Section_errors.html :l

  9.1 "Common problems"_9_1 :ulb,b

  9.2 "Reporting bugs"_9_2 :b

  9.3 "Error & warning messages"_9_3 :ule,b

  10.1 "Common problems"_10_1 :ulb,b

  10.2 "Reporting bugs"_10_2 :b

  10.3 "Error & warning messages"_10_3 :ule,b

"Future and history"_Section_history.html :l

  10.1 "Coming attractions"_10_1 :ulb,b

  10.2 "Past versions"_10_2 :ule,b

  11.1 "Coming attractions"_11_1 :ulb,b

  11.2 "Past versions"_11_2 :ule,b

:ole



:link(1_1,Section_intro.html#1_1)
@@ -166,12 +175,21 @@ listed above. 
:link(4_16,Section_howto.html#4_16)

:link(4_17,Section_howto.html#4_17)

:link(4_18,Section_howto.html#4_18)



:link(9_1,Section_errors.html#9_1)

:link(9_2,Section_errors.html#9_2)

:link(9_3,Section_errors.html#9_3)



:link(10_1,Section_history.html#10_1)

:link(10_2,Section_history.html#10_2)

:link(4_19,Section_howto.html#4_19)



:link(9_1,Section_python.html#9_1)

:link(9_2,Section_python.html#9_2)

:link(9_3,Section_python.html#9_3)

:link(9_4,Section_python.html#9_4)

:link(9_5,Section_python.html#9_5)

:link(9_6,Section_python.html#9_6)

:link(9_7,Section_python.html#9_7)



:link(10_1,Section_errors.html#10_1)

:link(10_2,Section_errors.html#10_2)

:link(10_3,Section_errors.html#10_3)



:link(11_1,Section_history.html#11_1)

:link(11_2,Section_history.html#11_2)



</BODY>

doc/Section_errors.html

+9 −9
Original line number Diff line number Diff line 
<HTML>

<CENTER><A HREF = "Section_modify.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -

<CENTER><A HREF = "Section_python.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -

<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_history.html">Next

Section</A> 

</CENTER>
@@ -11,18 +11,18 @@ Section</A> 


<HR>



<H3>9. Errors 

<H3>10. Errors 

</H3>

<P>This section describes the various kinds of errors you can encounter

when using LAMMPS.

</P>

9.1 <A HREF = "#9_1">Common problems</A><BR>

9.2 <A HREF = "#9_2">Reporting bugs</A><BR>

9.3 <A HREF = "#9_3">Error & warning messages</A> <BR>

10.1 <A HREF = "#10_1">Common problems</A><BR>

10.2 <A HREF = "#10_2">Reporting bugs</A><BR>

10.3 <A HREF = "#10_3">Error & warning messages</A> <BR>



<HR>



<A NAME = "9_1"></A><H4>9.1 Common problems 

<A NAME = "10_1"></A><H4>10.1 Common problems 

</H4>

<P>If two LAMMPS runs do not produce the same answer on different

machines or different numbers of processors, this is typically not a
@@ -81,7 +81,7 @@ decide if the WARNING is important or not. A WARNING message that is 
generated in the middle of a run is only printed to the screen, not to

the logfile, to avoid cluttering up thermodynamic output.  If LAMMPS

crashes or hangs without spitting out an error message first then it

could be a bug (see <A HREF = "#9_2">this section</A>) or one of the following

could be a bug (see <A HREF = "#10_2">this section</A>) or one of the following

cases:

</P>

<P>LAMMPS runs in the available memory a processor allows to be
@@ -112,7 +112,7 @@ buffering or boost the sizes of messages that can be buffered. 
</P>

<HR>



<A NAME = "9_2"></A><H4>9.2 Reporting bugs 

<A NAME = "10_2"></A><H4>10.2 Reporting bugs 

</H4>

<P>If you are confident that you have found a bug in LAMMPS, follow these

steps.
@@ -142,7 +142,7 @@ causing the problem. 
</P>

<HR>



<H4><A NAME = "9_3"></A>9.3 Error & warning messages 

<H4><A NAME = "10_3"></A>10.3 Error & warning messages 

</H4>

<P>These are two alphabetic lists of the <A HREF = "#error">ERROR</A> and

<A HREF = "#warn">WARNING</A> messages LAMMPS prints out and the reason why.  If the

doc/Section_errors.txt

+9 −9
Original line number Diff line number Diff line 
"Previous Section"_Section_modify.html - "LAMMPS WWW Site"_lws -

"Previous Section"_Section_python.html - "LAMMPS WWW Site"_lws -

"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next

Section"_Section_history.html :c
@@ -8,18 +8,18 @@ Section"_Section_history.html :c 


:line



9. Errors :h3

10. Errors :h3



This section describes the various kinds of errors you can encounter

when using LAMMPS.



9.1 "Common problems"_#9_1

9.2 "Reporting bugs"_#9_2

9.3 "Error & warning messages"_#9_3 :all(b)

10.1 "Common problems"_#10_1

10.2 "Reporting bugs"_#10_2

10.3 "Error & warning messages"_#10_3 :all(b)



:line



9.1 Common problems :link(9_1),h4

10.1 Common problems :link(10_1),h4



If two LAMMPS runs do not produce the same answer on different

machines or different numbers of processors, this is typically not a
@@ -78,7 +78,7 @@ decide if the WARNING is important or not. A WARNING message that is 
generated in the middle of a run is only printed to the screen, not to

the logfile, to avoid cluttering up thermodynamic output.  If LAMMPS

crashes or hangs without spitting out an error message first then it

could be a bug (see "this section"_#9_2) or one of the following

could be a bug (see "this section"_#10_2) or one of the following

cases:



LAMMPS runs in the available memory a processor allows to be
@@ -109,7 +109,7 @@ buffering or boost the sizes of messages that can be buffered. 


:line



9.2 Reporting bugs :link(9_2),h4

10.2 Reporting bugs :link(10_2),h4



If you are confident that you have found a bug in LAMMPS, follow these

steps.
@@ -139,7 +139,7 @@ As a last resort, you can send an email directly to the 


:line



9.3 Error & warning messages :h4,link(9_3)

10.3 Error & warning messages :h4,link(10_3)



These are two alphabetic lists of the "ERROR"_#error and

"WARNING"_#warn messages LAMMPS prints out and the reason why.  If the

doc/Section_history.html

+5 −5
Original line number Diff line number Diff line
@@ -9,18 +9,18 @@ 


<HR>



<H3>10. Future and history 

<H3>11. Future and history 

</H3>

<P>This section lists features we are planning to add to LAMMPS, features

of previous versions of LAMMPS, and features of other parallel

molecular dynamics codes I've distributed.

</P>

10.1 <A HREF = "#10_1">Coming attractions</A><BR>

10.2 <A HREF = "#10_2">Past versions</A> <BR>

11.1 <A HREF = "#11_1">Coming attractions</A><BR>

11.2 <A HREF = "#11_2">Past versions</A> <BR>



<HR>



<H4><A NAME = "10_1"></A>10.1 Coming attractions 

<H4><A NAME = "11_1"></A>11.1 Coming attractions 

</H4>

<P>The current version of LAMMPS incorporates nearly all the features

from previous parallel MD codes developed at Sandia.  These include
@@ -49,7 +49,7 @@ page</A> on the LAMMPS WWW site for more details. 
</UL>

<HR>



<H4><A NAME = "10_2"></A>10.2 Past versions 

<H4><A NAME = "11_2"></A>11.2 Past versions 

</H4>

<P>LAMMPS development began in the mid 1990s under a cooperative research

& development agreement (CRADA) between two DOE labs (Sandia and LLNL)

CRA Git | Maintained and supported by SUSTech CRA and CCSE