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