From 980c1a5c44de52bb3386dce2f67d087808b34d44 Mon Sep 17 00:00:00 2001 From: Erik Lindahl Date: Mon, 7 Jan 2013 01:06:06 +0100 Subject: [PATCH] Revert default rlist/rvdw/rcoulomb to valid values of 1.0 This reverts the part of commit 103d98cf31f064cce7c6ec14fcccd081aa2bbfac where the default values for rlist, rvdw, and rcoulomb were set to -1 to enable automatic optimization with verlet kernels and "force the user to think about the cutoff". The main reason is that this change breaks the default grompp files from working, which means it was no longer possible to use an empty mdp file for quick tests. However, I also think it is against the idea that the default values should be reasonable first tries - otherwise we might as well change every single default value in the mdp file to be invalid to force users to think. Change-Id: I1c40ea5fefc31c6635f21ceefe4da5c1c350b755 --- share/html/online/mdp_opt.html | 10 +++++----- src/kernel/readir.c | 6 +++--- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/share/html/online/mdp_opt.html b/share/html/online/mdp_opt.html index 88a27c21bf..6ef530faf6 100644 --- a/share/html/online/mdp_opt.html +++ b/share/html/online/mdp_opt.html @@ -542,7 +542,7 @@ For dynamics without temperature coupling or to override the buffer size, use verlet-buffer-drift=-1 and set rlist manually.
rlist: (1) [nm]
-
Cut-off distance for the short-range neighbor list, should be ≥ 0. +
Cut-off distance for the short-range neighbor list. With cutoff-scheme=Verlet, this is by default set by the verlet-buffer-drift option and the value of rlist is ignored.
@@ -716,8 +716,8 @@ affect the forces or the sampling.
rcoulomb-switch: (0) [nm]
where to start switching the Coulomb potential
-
rcoulomb: (-1) [nm]
-
distance for the Coulomb cut-off, should be ≥ 0
+
rcoulomb: (1) [nm]
+
distance for the Coulomb cut-off
epsilon-r: (1)
The relative dielectric constant. @@ -787,8 +787,8 @@ affect the forces or the sampling.
rvdw-switch: (0) [nm]
where to start switching the LJ potential
-
rvdw: (-1) [nm]
-
distance for the LJ or Buckingham cut-off, should be ≥ 0
+
rvdw: (1) [nm]
+
distance for the LJ or Buckingham cut-off
DispCorr:
diff --git a/src/kernel/readir.c b/src/kernel/readir.c index 0d47367058..3826994673 100644 --- a/src/kernel/readir.c +++ b/src/kernel/readir.c @@ -1621,7 +1621,7 @@ void get_ir(const char *mdparin,const char *mdparout, CTYPE ("a value of -1 means: use rlist"); RTYPE("verlet-buffer-drift", ir->verletbuf_drift, 0.005); CTYPE ("nblist cut-off"); - RTYPE ("rlist", ir->rlist, -1); + RTYPE ("rlist", ir->rlist, 1.0); CTYPE ("long-range cut-off for switched potentials"); RTYPE ("rlistlong", ir->rlistlong, -1); ITYPE ("nstcalclr", ir->nstcalclr, -1); @@ -1633,7 +1633,7 @@ void get_ir(const char *mdparin,const char *mdparout, EETYPE("coulomb-modifier", ir->coulomb_modifier, eintmod_names); CTYPE ("cut-off lengths"); RTYPE ("rcoulomb-switch", ir->rcoulomb_switch, 0.0); - RTYPE ("rcoulomb", ir->rcoulomb, -1); + RTYPE ("rcoulomb", ir->rcoulomb, 1.0); CTYPE ("Relative dielectric constant for the medium and the reaction field"); RTYPE ("epsilon-r", ir->epsilon_r, 1.0); RTYPE ("epsilon-rf", ir->epsilon_rf, 0.0); @@ -1642,7 +1642,7 @@ void get_ir(const char *mdparin,const char *mdparout, EETYPE("vdw-modifier", ir->vdw_modifier, eintmod_names); CTYPE ("cut-off lengths"); RTYPE ("rvdw-switch", ir->rvdw_switch, 0.0); - RTYPE ("rvdw", ir->rvdw, -1); + RTYPE ("rvdw", ir->rvdw, 1.0); CTYPE ("Apply long range dispersion corrections for Energy and Pressure"); EETYPE("DispCorr", ir->eDispCorr, edispc_names); CTYPE ("Extension of the potential lookup tables beyond the cut-off"); -- 2.22.0