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Merge "Merge branch release-5-1 into release-2016" into release-2016
2016-07-08
David van der Spoe
l
Merge "
M
erge branch release-
5
-1 into rel
e
as
e
-
2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
Szilárd Pál
l
Use
r
guide
c
larification
s
commit
|
commitdiff
|
tree
2016-07-07
B
e
rk Hess
Relax pu
l
l
PBC
c
h
eck
commit
|
commitdiff
|
tree
2016-07-03
Berk Hess
Ad
d
gro
m
pp check for pull group
commit
|
commitdiff
|
tree
2016-06-27
David va
n
der Spoel
Ma
d
e
gmx dos
w
ork again
.
commit
|
commitdiff
|
tree
2016-06-26
Berk Hess
Fix
v
site bug wit
h
MPI+OpenMP
commit
|
commitdiff
|
tree
2016-06-21
Berk Hess
Fix bug
with
fbposres+MPI+OpenMP
commit
|
commitdiff
|
tree
2016-05-30
Ber
k
H
e
s
s
A
d
d grompp
c
heck
for unbound atoms
commit
|
commitdiff
|
tree
2016-05-08
Mar
k
Abraham
Fi
x
cons
t
ants, unit
s
and conversion
factors
commit
|
commitdiff
|
tree
2016-03-23
Dav
i
d va
n
der Spoel
Re
m
oved srenew that wa
s
making array small
e
r incor
r
ectly
.
commit
|
commitdiff
|
tree
2016-01-20
Dav
i
d va
n
der Spoel
C
ouple of new q
u
o
te
s
commit
|
commitdiff
|
tree
2015-12-09
Teemu Murtol
a
S
plit
t
x
tdump
.
*, par
t
1
commit
|
commitdiff
|
tree
2015-12-05
Magnus Lundborg
Wri
t
e f
o
rces and velocities to
c
ompre
s
sed TNG
.
commit
|
commitdiff
|
tree
2015-11-24
David van der Spoel
F
ixes newl
y
introd
u
ced bug in mak
e
_nd
x
.
commit
|
commitdiff
|
tree
2015-11-23
David van
der Spoel
Moved
d
omde
c
structures o
u
t of comm
r
ec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
Davi
d
v
an d
e
r Spoel
Cleanups
in legacyhe
a
der/ty
p
e
s
/commr
e
c
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van der
Spoe
l
M
erged legacyhea
d
ers/
t
ypes/qmmmrec
.
h into mdlib/qmmm
.
h
commit
|
commitdiff
|
tree
2015-11-20
David van de
r
Spoel
Moved
l
egacyheaders/ty
p
es/group
.
h to mdt
y
pes
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoe
l
Me
r
g
e
d
legacyheade
r
s/types
/
ns
.
h a
n
d
nblist
.
h t
o
md
t
ypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van
der Spoel
Combine enu
m
s
.
h
a
n
d name
s
*
.
commit
|
commitdiff
|
tree
2015-11-20
Mark Abraham
Split wallcy
c
le interface
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Me
r
ged legacyheaders/nrnb
.
h and types/
n
r
n
b
.
h to gmx
l
ib
.
commit
|
commitdiff
|
tree
2015-11-20
David van
d
er Spoel
M
o
v
ed mdatom
.
h
f
rom le
g
a
cyheader/types t
o
mdtypes
.
commit
|
commitdiff
|
tree
2015-11-15
David van
d
er Spoel
Merged le
g
acyheaders/ty
p
es/sta
t
e
.
h into mdtypes/st
a
te
.
h
commit
|
commitdiff
|
tree
2015-11-14
Berk Hess
Optimized the bonde
d
thread f
o
rce
r
educti
o
n
commit
|
commitdiff
|
tree
2015-11-13
Da
v
id van
d
er Spoel
Moved genborn
.
h to mdlib
commit
|
commitdiff
|
tree
2015-11-12
David van der Spoel
Moved txtdump
.
* to fileio
.
commit
|
commitdiff
|
tree
2015-11-12
David van
d
er Spoel
M
ov
e
d co
p
yrite
.
* to
file
i
o
f
rom g
m
xlib and legacyheaders
.
commit
|
commitdiff
|
tree
2015-10-18
Da
v
id v
a
n de
r
Sp
o
el
Moved pbc/
c
ut-off
r
e
lated utilities from typedefs to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
Dav
i
d van der Spoel
Freed memory in legacy statistic
s
ro
u
t
i
nes
.
commit
|
commitdiff
|
tree
2015-10-15
B
erk
H
e
s
s
Fixed nbnxn_4x
N
performance regressi
o
n
commit
|
commitdiff
|
tree
2015-10-07
B
erk He
s
s
Fix bugs with intermol
interaction
s
and
D
D
commit
|
commitdiff
|
tree
2015-10-03
Davi
d
van der Spoel
Removed sim
p
le
.
h
commit
|
commitdiff
|
tree
2015-10-02
David van
d
er
Spoel
Remov
e
d simple
.
h from nb_kernel_avx_256_XX
commit
|
commitdiff
|
tree
2015-10-01
Teemu Murtola
Enable time un
i
t
and sele
c
tions
i
n ICom
m
andLin
e
OptionsModule
commit
|
commitdiff
|
tree
2015-09-30
Davi
d
van der Spoel
Removed t
y
pes/nblist
.
h and types/nsgrid
.
h from t
y
pedefs
.
h
commit
|
commitdiff
|
tree
2015-09-30
D
avid
van der
S
poel
Removed ty
p
es
/
mdatom
.
h
from typedef
s
.
h
commit
|
commitdiff
|
tree
2015-09-29
D
a
vi
d
van der S
p
oel
Removed types/inp
u
t
rec
.
h from typedefs
.
h and releted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
Mar
k
Abraham
Cle
a
n up of tables code
commit
|
commitdiff
|
tree
2015-09-29
Mark
A
b
r
a
ham
Move tables
.
c
to ne
w
module and C++
commit
|
commitdiff
|
tree
2015-09-29
Davi
d
v
an der Spoel
Fix
e
s bug
i
n the co
m
puta
t
ion of Coeffi
c
ient
o
f
Therma
l
.
.
.
commit
|
commitdiff
|
tree
2015-09-22
David
v
a
n der Spoel
R
e
move
d
four includ
e
s from leg
a
cyh
e
aders/typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
David
v
an der Spoel
Removed
leg
a
cyh
e
aders/types
/
commrec_
f
wd
.
h
f
rom
t
ypedef
.
h
commit
|
commitdiff
|
tree
2015-09-10
Dav
i
d van de
r
Spoel
Remove
d
<
s
ys/types
.
h> and "types/constr
.
h
" from typedef
s
commit
|
commitdiff
|
tree
2015-09-08
Davi
d
van der Spoel
Moved functions operatin
g
on for
c
erec to s
e
para
t
e heade
r
.
commit
|
commitdiff
|
tree
2015-09-04
Rossen
Ap
o
stolo
v
Co
n
verted
e
s
s
e
ntialdyn
a
mics mod
u
le to C++
.
commit
|
commitdiff
|
tree
2015-09-02
Bé
l
a Voß
Avo
i
d
i
n
teger o
v
erflo
w
i
n gm
x
_wham by using
g
mx_in
t
6
4
_t
.
commit
|
commitdiff
|
tree
2015-08-03
David van der
S
poel
Mad
e
outp
u
t from
du
m
ping ne
i
ghtborlist
s
easi
e
r
t
o
read
.
commit
|
commitdiff
|
tree
2015-07-29
Eri
k
Li
n
da
h
l
Moved another bunch
o
f
m
d
lib utils to C++
commit
|
commitdiff
|
tree
2015-07-29
Er
i
k Lindahl
Update naming
standards t
o
avoi
d
h
u
ngar
i
an not
a
tion
.
.
.
commit
|
commitdiff
|
tree
2015-07-24
Teemu Murtola
Rena
m
e
t
r
ni
o
.
*
to
trrio
.
*
commit
|
commitdiff
|
tree
2015-05-12
Jochen Hu
b
OpenMP p
a
ral
l
el
i
zation of g_wham
commit
|
commitdiff
|
tree
2015-04-09
Davi
d
van d
e
r Spoel
Clarified co
m
men
t
s for time-depen
d
ent electric
fields
.
commit
|
commitdiff
|
tree
2015-04-08
David v
a
n der Spoel
Fixed incorrect output of
g
b
_
algor
i
th
as s
a
_
algorithm
.
commit
|
commitdiff
|
tree
2014-10-28
Dav
i
d
van d
e
r
Spoel
Even more refreshing quotes
.
commit
|
commitdiff
|
tree
2014-09-22
Mark Abraham
More quote
s
commit
|
commitdiff
|
tree
2014-09-22
Erik Lindahl
More quotes
commit
|
commitdiff
|
tree
2014-09-19
Te
e
mu Murtola
Ad
d
support
for
cumulative
h
istograms
commit
|
commitdiff
|
tree
2014-09-17
Da
v
id van der Spoel
Merge release-5-0 in
t
o
master
commit
|
commitdiff
|
tree
2014-08-30
Davi
d
van der Spoel
Fixes issu
e
with vsiten and ve
r
let
b
uff
e
rs
.
commit
|
commitdiff
|
tree
2014-06-25
David
v
an d
e
r
Spoel
Added c
h
eck for domain decomposition an
d
shells
.
commit
|
commitdiff
|
tree
2014-06-22
David van der S
p
oel
Implement
e
d fatal
e
r
ror
f
or nstc
a
lce
n
ergy!=1
w
ith
shells
.
commit
|
commitdiff
|
tree
2014-06-13
Berk Hess
M
a
d
e
s
h
e
lls
w
ork
with the Verlet sch
e
m
e
commit
|
commitdiff
|
tree
2014-06-12
Berk He
s
s
Made gmxcheck -rmsd work agai
n
w
ith force
s
commit
|
commitdiff
|
tree
2014-06-12
Erik
L
ind
a
hl
Make su
r
e genrest
r
uses the disr
e
_up2 par
a
met
e
r
commit
|
commitdiff
|
tree
2014-06-12
E
rik
L
indahl
R
emo
v
ed und
o
cumented -map and -m
d
ata
o
pt
i
ons from g_sham
.
commit
|
commitdiff
|
tree
2014-06-12
Eri
k
Lindahl
Always w
r
ite
o
u
t
put
from genion
commit
|
commitdiff
|
tree
2014-06-11
David van der Spo
e
l
Fixes
bug
w
h
ere -e and -dt flags did not w
o
rk an
y
more
.
commit
|
commitdiff
|
tree
2014-06-11
Berk H
e
ss
Made repl_ex time step more r
e
adable
commit
|
commitdiff
|
tree
2014-06-07
Teemu Murtola
Improve
(Selection|FileName)OptionManager ha
n
d
l
i
n
g
commit
|
commitdiff
|
tree
2014-06-07
Te
e
mu M
u
r
t
o
la
R
e
pl
a
ce all command
li
n
e parsing with
O
ption
s
commit
|
commitdiff
|
tree
2014-06-07
Teem
u
Murtola
Move
r
esidu
e
ty
p
e handling to it
s
own file
.
commit
|
commitdiff
|
tree
2014-06-07
Teem
u
Murtola
Rem
o
ve support
f
o
r "old"
i
ndex file for
m
at
commit
|
commitdiff
|
tree
2014-05-31
Magnus Lundborg
Fix bug writi
n
g TN
G
out
p
ut from du
m
p
.
commit
|
commitdiff
|
tree
2014-05-31
M
a
gnus
L
undborg
Bug
f
ix in
the TNG libr
a
ry to improve read
i
ng
.
commit
|
commitdiff
|
tree
2014-05-24
Mark Abra
h
am
Move
tools
c
ode to where
i
t is used
commit
|
commitdiff
|
tree
2014-05-18
Teemu Murtola
Move 3dv
i
ew
.
* to p
r
ograms/view/
commit
|
commitdiff
|
tree
2014-05-16
D
a
v
id van der Spoel
Fixes a compli
c
a
t
ed bug in g_an
a
e
i
g
.
commit
|
commitdiff
|
tree
2014-03-17
Teemu
M
urt
o
l
a
Update manual
a
nalysis sectio
n
commit
|
commitdiff
|
tree
2014-02-21
Nin
a
Fisc
h
er
Add
e
d new am
b
er
9
9
s
b-ildn-bsc0 force field
.
commit
|
commitdiff
|
tree
2014-02-10
David van der Spoel
Moved conditio
n
al cmake
c
o
de for v
m
d
i
o
.
commit
|
commitdiff
|
tree
2014-01-19
Mark
Abraham
Clean up a
f
ter
g
mxcpp
commit
|
commitdiff
|
tree
2013-12-23
David van der Spoel
Fixed compilat
i
on issue
d
u
e
to
gcc4
.
8
commit
|
commitdiff
|
tree
2013-07-24
David
v
an der
Spoel
Fi
x
es
#
1312 u
n
initialized error in g_enemat
.
commit
|
commitdiff
|
tree
2013-05-16
D
a
vid v
a
n de
r
Spoel
Fixed
t
w
o compilation
issues
.
commit
|
commitdiff
|
tree
2013-05-02
David van
der Spoel
Fixes
#
1
23
8
g_
h
ydorder d
o
es not call set_p
b
c
.
commit
|
commitdiff
|
tree
2013-03-07
David van der Spoel
Fixes #1183 PBC bug
i
n g_mi
n
dist
commit
|
commitdiff
|
tree
2013-02-13
D
avid va
n
der Spoel
Plain tex
t
q
uotes
.
commit
|
commitdiff
|
tree
2012-11-26
David
v
an de
r
Spoel
F
i
x
es
#
1035
NaN in g_cluster outp
u
t
.
commit
|
commitdiff
|
tree
2012-11-20
David van der
Spo
e
l
Fixes bug in g_
h
bond that makes it
pro
d
uce f
a
ta
l
e
rror
.
commit
|
commitdiff
|
tree
2012-10-21
D
a
v
i
d van
der S
p
o
e
l
Fixe
d
Bug #59
3
a
b
out mem
o
ry
h
o
l
e
in t
r
jcat
.
commit
|
commitdiff
|
tree
2012-10-04
David van
d
er S
p
oel
Set ret
u
rn val
u
e to FALSE (0) in
estim
a
te_
d
t
i
n libxdrf
.
c
commit
|
commitdiff
|
tree
2012-09-07
Davi
d
van der Spoel
Adapt
e
d NMR related
d
ata
t
o new pd
b
form
a
t
.
commit
|
commitdiff
|
tree
2012-09-04
D
avid van d
e
r
S
poel
Made tu
t
orial s
l
ightly less confusing
.
commit
|
commitdiff
|
tree
2012-08-16
Da
v
id van der Spoel
Optional co
m
putation of fluct
.
p
r
o
p
s in
g
_ene
r
gy
.
Fixes
.
.
.
commit
|
commitdiff
|
tree
2012-06-30
David van der S
p
oel
Fixed bug i
n
f
r
ee energy
c
a
lculation f
o
r
M
orse potentials
commit
|
commitdiff
|
tree
2012-06-21
David van der Spoel
F
i
xes #9
6
1 - Shake reports
wrong error
commit
|
commitdiff
|
tree
2012-03-17
David va
n
de
r
Spo
e
l
Remo
v
ed
qhop
f
iles from this branch
.
commit
|
commitdiff
|
tree
2012-03-10
David van de
r
Spoel
Vibrati
o
n
s
pec
t
ra from
velocity ACF
o
r Normal modes
.
commit
|
commitdiff
|
tree
2012-01-31
David van
der Spoel
Changed orde
r
of parame
t
ers in t
o
p file
commit
|
commitdiff
|
tree
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