diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 1c9a9fecb2..c4eb8747b6 100644 --- a/doc/Section_commands.html +++ b/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:
-variable a equal 2
-variable b2 equal 4
-print "B2 = ${b$a}"
+variable a equal 2
+variable b2 equal 4
+region 1 block ${b$a} 2 INF INF EDGE EDGE
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
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt
index 16940c4f62..c6d4b3d655 100644
--- a/doc/Section_commands.txt
+++ b/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
diff --git a/doc/Section_start.html b/doc/Section_start.html
index a9b63ac6e4..b81fbc11c2 100644
--- a/doc/Section_start.html
+++ b/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.
+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
+
+/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
+
As an example, here is how to build and install the MPICH
library, a popular open-source version of MPI, distributed by
Argonne National Labs, as a shared library in the default
diff --git a/doc/Section_start.txt b/doc/Section_start.txt
index a33f41b9ae..e89ec84a6c 100644
--- a/doc/Section_start.txt
+++ b/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
diff --git a/doc/pair_coul.html b/doc/pair_coul.html
index 4edb0835ba..466dfd33c1 100644
--- a/doc/pair_coul.html
+++ b/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.
-These potentials are designed to be combined with other pair
+
+
+Note that these potentials are designed to be combined with other pair
potentials via the pair_style hybrid/overlay
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 command as in the examples
diff --git a/doc/pair_coul.txt b/doc/pair_coul.txt
index bdae57bbae..46fbf307f0 100644
--- a/doc/pair_coul.txt
+++ b/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