From d44539ba276bd0883a49c03475e46c1f45036690 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Tue, 15 Oct 2013 12:46:29 +0200
Subject: [PATCH] A couple of fixes in doc
---
developer-doc/mdTemplate.txt | 3 ++-
src/core/PlumedMain.cpp | 1 +
2 files changed, 3 insertions(+), 1 deletion(-)
diff --git a/developer-doc/mdTemplate.txt b/developer-doc/mdTemplate.txt
index 0c22d01f1..21f90bd08 100644
--- a/developer-doc/mdTemplate.txt
+++ b/developer-doc/mdTemplate.txt
@@ -185,7 +185,8 @@ plumed_cmd(plumedmain,"setMDEnergyUnits",&energyUnits); // Pass a pointer
plumed_cmd(plumedmain,"setMDLengthUnits",&lengthUnits); // Pass a pointer to the conversion factor between the length unit used in your code and nm
plumed_cmd(plumedmain,"setMDTimeUnits",&timeUnits); // Pass a pointer to the conversion factor between the time unit used in your code and ps
plumed_cmd(plumedmain,"setPlumedDat",&plumedInput); // Pass the name of the plumed input file from the md code to plumed
-plumed_cmd(plumedmain,"setMPIComm",&MPI_COMM_WORLD); // Pass a pointer to the MPI communicator to plumed?
+plumed_cmd(plumedmain,"setMPIComm",&MPI_COMM_WORLD); // Pass a pointer to the MPI communicator to plumed
+// notice that from fortran the command "setMPIFComm" should be used instead
plumed_cmd(plumedmain,"setNatoms",&natoms); // Pass a pointer to the number of atoms in the system to plumed
plumed_cmd(plumedmain,"setMDEngine","gromacs"); // Pass the name of your md engine to plumed (now it is just a label)
plumed_cmd(plumedmain,"setLog",fplog); // Pass the file on which to write out the plumed log (if the file is already open)
diff --git a/src/core/PlumedMain.cpp b/src/core/PlumedMain.cpp
index b19ca1a23..6e1e0f10e 100644
--- a/src/core/PlumedMain.cpp
+++ b/src/core/PlumedMain.cpp
@@ -293,6 +293,7 @@ void PlumedMain::cmd(const std::string & word,void*val){
CHECK_NOTINIT(initialized,word);
CHECK_NULL(val,word);
stopFlag=static_cast<int*>(val);
+// other commands that should be used after initialization:
} else if(word=="getExchangesFlag"){
CHECK_INIT(initialized,word);
CHECK_NULL(val,word);
--
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