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Fix small leaks in do_md cleanup
2018-12-26
Kevin
B
oyd
Fi
x
small
l
e
a
ks in do_md cle
a
nu
p
commit
|
commitdiff
|
tree
2018-12-22
David van d
e
r
Sp
o
e
l
Revert "Removed t_
t
opolog
y
fr
o
m gmx msd"
commit
|
commitdiff
|
tree
2018-12-05
Davi
d
van der
S
po
e
l
Adde
d
n
e
w testing
c
ode for n
o
rmal
m
od
e
analysis
.
commit
|
commitdiff
|
tree
2018-12-04
David van der Spo
e
l
Small
update to
m
drun t
e
sts
.
commit
|
commitdiff
|
tree
2018-12-04
Da
v
id van der Sp
o
el
Removed gmx mor
p
h
commit
|
commitdiff
|
tree
2018-12-04
Dav
i
d van
d
er Spoel
Rem
o
ved
gmx dyndom
commit
|
commitdiff
|
tree
2018-12-04
Davi
d
va
n
der Spoel
R
e
moved gmx anadock
commit
|
commitdiff
|
tree
2018-11-21
David van der Spoel
Merge branc
h
'release-2019
'
commit
|
commitdiff
|
tree
2018-11-19
Mark Abraham
F
i
x ineffi
c
ient sh
e
ll minimi
z
at
i
on
commit
|
commitdiff
|
tree
2018-11-18
David va
n
der
S
poe
l
A
dded ci
t
at
i
on for
n
ew analysis functionality
.
commit
|
commitdiff
|
tree
2018-11-08
Pa
u
l Bauer
Actu
a
lly fix gmx helix
segmentation fault
commit
|
commitdiff
|
tree
2018-10-15
Mark Abraham
I
mprov
e
r
o
bustness o
f
end-
t
o-end testi
n
g
commit
|
commitdiff
|
tree
2018-06-22
Mark Abr
a
ham
Update
e
nergy
a
nd trajecto
r
y
frame t
y
pes
commit
|
commitdiff
|
tree
2018-06-12
M
ark Abraham
Prepare for
GR
O
MACS 2
0
1
9
relea
s
e notes
commit
|
commitdiff
|
tree
2018-06-12
Davi
d
va
n
der Spo
e
l
Let
gmx
n
meig
print
t
hermochemis
t
ry
.
commit
|
commitdiff
|
tree
2018-03-16
David v
a
n der Spoel
Split off entropy calculation to separat
e
file
.
commit
|
commitdiff
|
tree
2018-01-04
Erik Lindah
l
Improve
f
rame
t
ime/step handl
i
ng
in t
r
j
conv
commit
|
commitdiff
|
tree
2018-01-03
Erik Lindah
l
Fix trjc
o
nv fo
r
tdum
p
<
frame timestep
commit
|
commitdiff
|
tree
2018-01-01
Erik Lindahl
Fix
gmx d
e
nsity for n
o
n
-mass
ca
l
culations
commit
|
commitdiff
|
tree
2017-12-28
David
v
an der Spoel
Fixes and updates for
x
plor2gml
.
p
l and at
o
m_nom
.
t
bl
commit
|
commitdiff
|
tree
2017-10-30
Dav
i
d van der Spoel
Fixed md
p
outp
u
t
f
rom electric fiel
d
c
ode
.
commit
|
commitdiff
|
tree
2017-10-27
Aleksei I
u
pinov
R
e
m
ov
e
unused
PME grid dump debug funct
i
ons
commit
|
commitdiff
|
tree
2017-10-17
D
a
vid van der Spoel
Fix
e
d
m
iss
i
ng entries
i
n
nrnb arr
a
ys
.
commit
|
commitdiff
|
tree
2017-09-04
Teemu Murtola
Introdu
c
e se
l
f
-
pa
i
rs sear
c
h in nbse
a
rch
commit
|
commitdiff
|
tree
2017-09-04
T
e
emu
M
urto
l
a
Refactor analysis nbsearc
h
tests
commit
|
commitdiff
|
tree
2017-08-09
Roland
S
chu
l
z
Use tabl
e
Ewald for Skylak
e
commit
|
commitdiff
|
tree
2017-08-03
David van der Spoe
l
Fixed bug in gmx dis
r
es in
d
e
xing arr
a
y
s
.
commit
|
commitdiff
|
tree
2017-08-02
Berk Hes
s
Make
l
oop va
r
iables in ori
r
es
.
cpp loca
l
commit
|
commitdiff
|
tree
2017-08-02
Be
r
k Hess
Add c
h
eck fo
r
n
r
o
f
orientati
o
n restraints
commit
|
commitdiff
|
tree
2017-07-19
Dav
i
d van der Spo
e
l
Fixed tes
t
-order dependency in g
m
xpreprocess tests
.
commit
|
commitdiff
|
tree
2017-07-19
David van de
r
S
p
oel
Fix non-reproducability
of cl
u
stsize tests
.
commit
|
commitdiff
|
tree
2017-04-29
Carsten Kut
z
ner
Minor
header file cleanup in ED
,
IMD and CompE
L
modules
commit
|
commitdiff
|
tree
2017-04-22
Mark Abraha
m
Clean
u
p memory
u
s
age
with oenv an
d
xvg writing
commit
|
commitdiff
|
tree
2017-03-13
Teemu Murtola
Improve o
p
tion
s
u
pport & tests fo
r
key-v
a
lue trees
commit
|
commitdiff
|
tree
2017-03-13
Teemu Mu
r
tola
Rem
o
ve manual alignment f
r
om InMemor
y
Seri
a
l
i
z
e
r
commit
|
commitdiff
|
tree
2017-03-12
Tee
m
u
M
u
r
t
ola
Con
s
i
s
tent Text
W
riter trailing whitespace
handling
commit
|
commitdiff
|
tree
2017-03-12
David van der Spoel
Added test
s
for gmx clust
s
iz
e
.
commit
|
commitdiff
|
tree
2017-03-04
V
edran Mil
e
tić
Docum
e
nt
that
w
e no
w
suppor
t
AMD GCN on Mesa/LLV
M
commit
|
commitdiff
|
tree
2017-02-28
Berk H
e
ss
Add
l
oad b
a
lance
f
r
a
ction to DLB print
commit
|
commitdiff
|
tree
2017-02-28
Teemu
M
urtola
More documentat
i
o
n
for ke
y
-val
u
e
t
rees
commit
|
commitdiff
|
tree
2017-02-27
Da
v
id v
a
n der
Spoel
Fixes bug
in gmx sol
v
ate with -shell t
h
at yielded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-09
Alek
s
ei
I
u
pi
n
ov
Add ini
t
ializat
i
on to dvdlambda in bonded fo
r
ces t
e
sts
commit
|
commitdiff
|
tree
2017-02-08
Mark Abraham
Remove
d
o
cs fo
r
unimplemented tr
j
con
v
-
c
l
usterc
e
nter
commit
|
commitdiff
|
tree
2017-02-02
Mark
Abraham
Clar
i
fy
use
o
f ta
u
-p and pcoupltype
commit
|
commitdiff
|
tree
2017-01-30
M
a
rk
A
braham
D
o
n
'
t pr
i
n
t inval
i
d perform
a
nce data
commit
|
commitdiff
|
tree
2016-12-14
Mark A
b
r
a
ham
Fix m
i
slea
d
ing paralleliz
a
ti
o
n docs
f
or gmx w
h
am
commit
|
commitdiff
|
tree
2016-11-21
Aleksei I
u
pin
o
v
Move
hardcod
e
d PME grid indexi
n
g constants into header
commit
|
commitdiff
|
tree
2016-11-18
D
avid van d
e
r Spoel
A
dd
e
d f
i
rst tes
t
s o
f
bonded force function
s
.
commit
|
commitdiff
|
tree
2016-11-16
Mark Abraham
Enh
a
nced Array
R
e
f
commit
|
commitdiff
|
tree
2016-11-16
Mark A
b
r
aham
Created pad
d
edvector
.
h
commit
|
commitdiff
|
tree
2016-10-24
Teemu Murtola
Electric
f
ield mdp
p
arsin
g
using options
commit
|
commitdiff
|
tree
2016-10-24
Teemu Mu
r
tola
S
u
pport for default
v
alues
f
rom Options
t
o
KeyValueTre
e
commit
|
commitdiff
|
tree
2016-10-14
Berk Hess
Appl
y
Beren
d
sen
P-couple at nstpcouple steps
commit
|
commitdiff
|
tree
2016-10-14
Te
e
mu Murt
o
la
U
s
e g
m
x_mtop_t in selections
,
p
art 3
commit
|
commitdiff
|
tree
2016-10-13
Teemu Murtola
Getter
fo
r
m
apped paths from KeyValueTr
e
eTr
a
nsform
commit
|
commitdiff
|
tree
2016-10-08
Berk
H
e
ss
Ad
d
re
a
dConfAndT
o
p
ology
commit
|
commitdiff
|
tree
2016-10-03
Philip
L
oche
EW3DC for non-neutral systems
commit
|
commitdiff
|
tree
2016-10-01
Ber
k
Hess
Fix inpu
t
rec initialization in
4 tools
commit
|
commitdiff
|
tree
2016-09-29
Berk Hess
U
s
e
std::vector in
t
_state
commit
|
commitdiff
|
tree
2016-09-29
B
e
rk Hes
s
Add flags
f
or optional t
_
atoms entries
commit
|
commitdiff
|
tree
2016-09-20
Berk Hess
Rem
o
ve
state duplication
i
n
serial ru
n
s
commit
|
commitdiff
|
tree
2016-09-20
D
a
vid van
d
er
Spoel
Made correlation f
u
nction ro
u
tine use std::vector
commit
|
commitdiff
|
tree
2016-09-16
Berk H
e
ss
Made di
s
tance
rest
r
aint
s
work w
i
th t
h
reads
and DD
commit
|
commitdiff
|
tree
2016-09-15
Aleksei Iu
p
inov
Move the
P
ME Ewald
coeffic
i
ents to the PME s
t
ructure
commit
|
commitdiff
|
tree
2016-09-13
Rolan
d
Schulz
Tidy:
modernize-use
-
empl
a
ce
commit
|
commitdiff
|
tree
2016-09-13
Berk H
e
ss
Change ED and swa
p
state to pointers i
n
t_s
t
ate
commit
|
commitdiff
|
tree
2016-09-11
V
e
dran Miletić
Pr
i
nt OpenCL er
r
or string instead of error c
o
de
commit
|
commitdiff
|
tree
2016-09-10
B
e
r
k Hess
Remove cont
i
nua
t
i
o
n fro
m
convert
_
tpr
commit
|
commitdiff
|
tree
2016-09-10
Aleksei
I
u
pinov
F
i
x
PME da
t
a
destru
c
t
or
n
ot
b
e
i
n
g
called
commit
|
commitdiff
|
tree
2016-09-05
David van der Spoel
Merge "Mer
g
e branch release
-
2016"
commit
|
commitdiff
|
tree
2016-08-27
Szil
á
rd P
á
ll
Make
ASAN/TS
A
N/MSAN bu
i
ld typ
e
s ea
s
ier to discover
commit
|
commitdiff
|
tree
2016-08-27
Ma
r
k Abr
a
ham
St
o
p using gmx_f
a
tal in gro
m
pp
commit
|
commitdiff
|
tree
2016-08-27
Teemu Murtola
Support KeyValueTr
e
e objects in refdata
commit
|
commitdiff
|
tree
2016-08-27
Berk Hess
Reduce rou
n
ding err
o
rs in SETTLE
commit
|
commitdiff
|
tree
2016-08-27
Ro
l
a
nd Schulz
Fix build with
G
MX
_
USE_TNG=off
commit
|
commitdiff
|
tree
2016-08-24
David v
a
n
d
er
S
p
o
e
l
Ad
d
ed documentati
o
n
for shell potentia
l
s
.
commit
|
commitdiff
|
tree
2016-07-31
D
a
vid
v
an
d
er Spoel
Mer
g
e "Merge branch
release-5-1 into release-2
0
1
6"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
V
edran
M
iletić
Print
w
o
rking di
r
befor
e
c
o
mmand li
n
e
commit
|
commitdiff
|
tree
2016-07-08
Davi
d
van
d
e
r Spoel
Merge
"
Merge branch release-5-1 into release-
2
0
16"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
Szilá
r
d
Páll
User
g
uide
clari
f
i
cations
commit
|
commitdiff
|
tree
2016-07-07
Berk Hess
R
e
lax pull PBC check
commit
|
commitdiff
|
tree
2016-07-03
Berk Hess
Add
g
rom
p
p check for pull
g
roup
commit
|
commitdiff
|
tree
2016-06-27
David van
der Spoel
Made gmx dos work again
.
commit
|
commitdiff
|
tree
2016-06-26
Berk Hess
Fix vsite
bug with MP
I
+OpenMP
commit
|
commitdiff
|
tree
2016-06-21
B
erk He
s
s
Fix b
u
g with f
b
posres+MPI+
O
penMP
commit
|
commitdiff
|
tree
2016-05-30
Ber
k
Hess
Add g
r
ompp check for unbound atoms
commit
|
commitdiff
|
tree
2016-05-08
Mark Abraham
Fix constant
s
, uni
t
s and conversion factors
commit
|
commitdiff
|
tree
2016-03-23
Dav
i
d van de
r
Spoel
Removed srenew that
was making array smalle
r
incor
r
ectly
.
commit
|
commitdiff
|
tree
2016-01-20
David van der Spoel
Coupl
e
of
n
ew quotes
commit
|
commitdiff
|
tree
2015-12-09
Teemu Murto
l
a
Split txtdum
p
.
*, p
a
rt
1
commit
|
commitdiff
|
tree
2015-12-05
M
a
gnus
Lundborg
Write forces
a
n
d
velocit
i
e
s
to
compre
s
sed TN
G
.
commit
|
commitdiff
|
tree
2015-11-24
David van der Spoe
l
Fi
x
es newly
intr
o
du
c
ed bug in make_
n
dx
.
commit
|
commitdiff
|
tree
2015-11-23
David van der Sp
o
el
Moved domde
c
structures out of
commrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David van d
e
r Spoel
Cle
a
nups in legacyheader/types/commrec
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van
der Spoel
Me
r
ged
l
egacyheaders/types
/
qmmmrec
.
h
int
o
m
dlib/
q
mmm
.
h
commit
|
commitdiff
|
tree
2015-11-20
David van
d
er Spoel
Move
d
l
e
gacyheaders/types/group
.
h
t
o mdtype
s
.
commit
|
commitdiff
|
tree
2015-11-20
Dav
i
d v
a
n der Spoel
Merged l
e
gacyheade
r
s/
t
ype
s
/ns
.
h and nblist
.
h to
mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Comb
i
ne enums
.
h and n
a
mes*
.
commit
|
commitdiff
|
tree
2015-11-20
Mar
k
Abrah
a
m
S
p
l
it wallcycle in
t
erface
commit
|
commitdiff
|
tree
2015-11-20
David
van
de
r
S
p
oel
Merged legacyheaders/nr
n
b
.
h
and types/n
r
nb
.
h to gmxlib
.
commit
|
commitdiff
|
tree
next