git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13232 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_commands.html

@@ -136,9 +136,9 @@ variable X delete
 contain nested $ characters for other variables to substitute for.
 Thus you cannot do this:
 </P>
-<PRE>variable        a equal 2
-variable        b2 equal 4
-print           "B2 = ${b$a}" 
+<PRE>variable   a equal 2
+variable   b2 equal 4
+region     1 block ${b$a} 2 INF INF EDGE EDGE 
 </PRE>
 <P>Nor can you specify this $($x-1.0) for an immediate variable, but
 you could use $(v_x-1.0), since the latter is valid syntax for an

doc/Section_commands.txt

@@ -132,9 +132,9 @@ Note that neither the curly-bracket or immediate form of variables can
 contain nested $ characters for other variables to substitute for.
 Thus you cannot do this:
 
-variable        a equal 2
-variable        b2 equal 4
-print           "B2 = $\{b$a\}" :pre
+variable   a equal 2
+variable   b2 equal 4
+region     1 block $\{b$a\} 2 INF INF EDGE EDGE :pre
 
 Nor can you specify this $($x-1.0) for an immediate variable, but
 you could use $(v_x-1.0), since the latter is valid syntax for an

doc/Section_start.html

@@ -1087,6 +1087,19 @@ error.  This means you will need to install a shared library version
 of the auxiliary library.  The build instructions for the library
 should tell you how to do this.
 </P>
+<P>Here is an example of such errors when the system FFTW or provided
+lib/colvars library have not been built as shared libraries:
+</P>
+<PRE>/usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation
+R_X86_64_32 against `.rodata' can not be used when making a shared
+object; recompile with -fPIC
+/usr/local/lib/libfftw3.a: could not read symbols: Bad value 
+</PRE>
+<PRE>/usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o):
+relocation R_X86_64_32 against `__pthread_key_create' can not be used
+when making a shared object; recompile with -fPIC
+../../lib/colvars/libcolvars.a: error adding symbols: Bad value 
+</PRE>
 <P>As an example, here is how to build and install the <A HREF = "http://www-unix.mcs.anl.gov/mpi">MPICH
 library</A>, a popular open-source version of MPI, distributed by
 Argonne National Labs, as a shared library in the default

doc/Section_start.txt

@@ -1079,6 +1079,19 @@ error.  This means you will need to install a shared library version
 of the auxiliary library.  The build instructions for the library
 should tell you how to do this.
 
+Here is an example of such errors when the system FFTW or provided
+lib/colvars library have not been built as shared libraries:
+
+/usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation
+R_X86_64_32 against `.rodata' can not be used when making a shared
+object; recompile with -fPIC
+/usr/local/lib/libfftw3.a: could not read symbols: Bad value :pre
+
+/usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o):
+relocation R_X86_64_32 against `__pthread_key_create' can not be used
+when making a shared object; recompile with -fPIC
+../../lib/colvars/libcolvars.a: error adding symbols: Bad value :pre
+
 As an example, here is how to build and install the "MPICH
 library"_mpich, a popular open-source version of MPI, distributed by
 Argonne National Labs, as a shared library in the default

doc/pair_coul.html

@@ -248,11 +248,14 @@ cutoff + 2*qdist, to shrink the size of the neighbor list.  This leads
 to slightly larger cost for the long-range calculation, so you can
 test the trade-off for your model.
 </P>
-<P>These potentials are designed to be combined with other pair
+<HR>
+
+<P>Note that these potentials are designed to be combined with other pair
 potentials via the <A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A>
 command.  This is because they have no repulsive core.  Hence if they
 are used by themselves, there will be no repulsion to keep two
-oppositely charged particles from overlapping each other.
+oppositely charged particles from moving arbitrarily close to each
+other.
 </P>
 <P>The following coefficients must be defined for each pair of atoms
 types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples

doc/pair_coul.txt

@@ -222,11 +222,14 @@ cutoff + 2*qdist, to shrink the size of the neighbor list.  This leads
 to slightly larger cost for the long-range calculation, so you can
 test the trade-off for your model.
 
-These potentials are designed to be combined with other pair
+:line
+
+Note that these potentials are designed to be combined with other pair
 potentials via the "pair_style hybrid/overlay"_pair_hybrid.html
 command.  This is because they have no repulsive core.  Hence if they
 are used by themselves, there will be no repulsion to keep two
-oppositely charged particles from overlapping each other.
+oppositely charged particles from moving arbitrarily close to each
+other.
 
 The following coefficients must be defined for each pair of atoms
 types via the "pair_coeff"_pair_coeff.html command as in the examples