From bc8f90affc3caa9e17c220f86e71866e18fcbf03 Mon Sep 17 00:00:00 2001 From: Giovanni Bussi <giovanni.bussi@gmail.com> Date: Thu, 16 Jun 2016 12:34:42 +0200 Subject: [PATCH] Added doc --- developer-doc/mdTemplate.txt | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/developer-doc/mdTemplate.txt b/developer-doc/mdTemplate.txt index 96058d85e..2a3afe66b 100644 --- a/developer-doc/mdTemplate.txt +++ b/developer-doc/mdTemplate.txt @@ -212,6 +212,9 @@ plumed_cmd(plumedmain,"setKbT",&kbT); // Pointer to a r // This is valid only if API VERSION > 2 plumed_cmd(plumedmain,"setRestart",&res); // Pointer to an integer saying if we are restarting (zero means no, one means yes) +// This is valid only if API VERSION > 3 +plumed_cmd(plumedmain,"readInputLine","d: DISTANCE ATOMS=1,2");// Read a single input line directly from a string + // Calls to do the actual initialization (all the above commands must appear before this call) plumed_cmd(plumedmain,"init",NULL); // Do all the initialization of plumed plumed_cmd(plumedmain,"read",read); // Read the plumed input. N.B. This is called during init and so this call is only required in special cases. @@ -257,6 +260,12 @@ plumed_cmd(plumedmain,"calc",NULL); // Calculate and ap // One can break up the "calc" command in two parts: plumed_cmd(plumedmain,"prepareCalc",NULL); // Prepare to do a calculation by requesting all the atomic positions from the MD code plumed_cmd(plumedmain,"performCalc",NULL); // Use the atomic positions collected during prepareCalc phase to calculate colvars and biases. +// The "performCalc" step can be further split into: +// This is valid only if API VERSION > 3 +plumed_cmd(plumedmain,"performCalcNoUpdate",NULL); // Same as "performCalc", skipping the update phase. Could be called multiple time per step +// This is valid only if API VERSION > 3 +plumed_cmd(plumedmain,"update",NULL); // Only performs the update phase. Should be called once per step + // After the first part it will be possible to ask PLUMED e.g. if the energy is required with plumed_cmd(plumedmain,"isEnergyNeeded,&flag); // assuming flag is an int, that will be set to 0 if energy is not needed and 1 if it is needed -- GitLab