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Disallow -skip values <= 0 for gmx trjconv.
2018-04-17
Viveca Linda
h
l
Disa
l
low
-
skip val
u
es <= 0 for gmx trjconv
.
commit
|
commitdiff
|
tree
2018-04-17
Paul Bauer
Fix le
g
acy topology memory error
commit
|
commitdiff
|
tree
2018-04-17
Mark
A
bra
h
am
Shift
pe
r
-st
e
p
control logic to do_md
commit
|
commitdiff
|
tree
2018-04-17
Mar
k
Ab
r
aham
Break
apar
t
u
p
date_constraints
commit
|
commitdiff
|
tree
2018-04-16
Szilá
r
d Páll
Ad
d
post-submit tes
t
with hwloc off
commit
|
commitdiff
|
tree
2018-04-16
Berk Hess
M
o
ve natoms_mol out of gm
x
_mo
l
block_t
commit
|
commitdiff
|
tree
2018-04-16
M
a
rk Ab
r
a
h
a
m
Updated mdrun comparison infr
a
structure
commit
|
commitdiff
|
tree
2018-04-13
M
ark Abrah
a
m
Clean up c
o
nstraints cod
e
commit
|
commitdiff
|
tree
2018-04-12
Mark Abraham
Rem
o
ve use of where(), if
D
EBUG etc
.
commit
|
commitdiff
|
tree
2018-04-12
M
a
r
k Abraham
R
e
or
g
anize e
n
ergy eva
l
u
ation for EM
commit
|
commitdiff
|
tree
2018-04-10
Al
e
k
s
e
i
Iupinov
Prevent O
p
en
C
L
timing mem
o
ry leak
commit
|
commitdiff
|
tree
2018-04-09
Berk Hess
Convert
g
mx_molblock_t to C++
commit
|
commitdiff
|
tree
2018-04-05
Mar
k
Abr
a
ham
Simplifi
e
d handling of simul
a
tion runners
commit
|
commitdiff
|
tree
2018-04-05
Mark Abraham
Create gromacs/mdrun module and move cod
e
there
commit
|
commitdiff
|
tree
2018-04-05
S
zilá
r
d
P
áll
Refactor cj preload in the non
b
on
d
ed O
p
enCL kernels
commit
|
commitdiff
|
tree
2018-04-04
Mar
k
A
b
raham
Quiet check
p
o
i
nt r
e
ading
commit
|
commitdiff
|
tree
2018-04-04
Pas
c
al Merz
Move
ch
e
ckNumber
O
fBondedInter
a
ct
i
ons
commit
|
commitdiff
|
tree
2018-04-03
Berk
H
ess
Con
v
e
r
t
gmx_mtop
_
t
t
o C++
commit
|
commitdiff
|
tree
2018-04-03
Mark Abra
h
am
R
emove l
e
ftover menti
o
n of t
w
in-range scheme
commit
|
commitdiff
|
tree
2018-04-03
M
a
rk Abraham
Merge "Merge b
r
a
n
c
h
release-2018"
commit
|
commitdiff
|
tree
2018-03-29
B
e
rk H
e
ss
Move fi
l
e opening out of
ini
t
_pull()
commit
|
commitdiff
|
tree
2018-03-29
Sz
i
lárd Páll
Tweak/ena
b
le i
c
c
1
8
p
ost-submit tests
commit
|
commitdiff
|
tree
2018-03-29
Magnus
L
un
d
borg
Improved check of if only
f
orces ar
e
computed
i
n
d
o_pairs()
commit
|
commitdiff
|
tree
2018-03-29
Pau
l
Bauer
Fix cmake
S
phin
x
detection for versions >1
.
6
.
4
commit
|
commitdiff
|
tree
2018-03-29
Szilárd Páll
Switch
C
U
DA 9
.
0/g
c
c 5 t
e
s
t to
CUDA 9
.
1/gcc
6
commit
|
commitdiff
|
tree
2018-03-29
Berk H
e
ss
Modul
a
rize pull
_
c
o
o
rd_
w
ork_
t
commit
|
commitdiff
|
tree
2018-03-28
Mark Abr
a
ham
Free more m
e
mory in gro
m
pp an
d
mdr
u
n
commit
|
commitdiff
|
tree
2018-03-28
Berk Hes
s
R
e
m
ove mols from g
m
x_
m
top_t
commit
|
commitdiff
|
tree
2018-03-28
Mark Abr
a
ham
Mer
g
e
branch
r
e
l
e
a
se-2018
commit
|
commitdiff
|
tree
2018-03-27
M
a
r
k
A
b
raham
Clarified
m
d
p options rela
t
ing to bonds
commit
|
commitdiff
|
tree
2018-03-27
Mark Abraham
More gcc-8 fixes for
P
OWER
commit
|
commitdiff
|
tree
2018-03-21
Davi
d
van der Spoel
Renamed en
t
r
o
py
.
* to th
e
r
moc
h
emistry
.
*
commit
|
commitdiff
|
tree
2018-03-21
M
a
rk Abr
a
ham
Versio
n
2018
.
1
commit
|
commitdiff
|
tree
2018-03-21
Mark
Abraha
m
Mer
g
e "M
e
rge br
a
nch release
-
2016 into release-2018
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
Mark
A
braham
Up
d
a
te rel
e
ase n
o
tes for 2018
.
1
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Me
r
ge b
r
anch rel
e
a
se-201
6
into rele
a
se-2018
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraha
m
Update use
of gpu_id in Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Ber
k
Hess
D
i
sa
l
low single s
i
mula
t
io
n
wi
t
h mul
t
isim
commit
|
commitdiff
|
tree
2018-03-20
M
a
rk Abraham
Upda
t
e
u
se of gpu_id
in Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Update
u
se of gpu_id in Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Add helper function to
make a ve
c
tor from an Arra
y
Ref
commit
|
commitdiff
|
tree
2018-03-19
Mark Abraham
F
i
x VSX
SIMD with gcc 8
commit
|
commitdiff
|
tree
2018-03-16
Pa
u
l Bauer
Only free topology
w
hen allocated
commit
|
commitdiff
|
tree
2018-03-16
Berk H
e
ss
Cor
r
e
ct PMF sign err
o
r
in AWH b
i
as sharing
commit
|
commitdiff
|
tree
2018-03-14
Berk
Hess
Improve in
t
er-simulat
i
o
n signal
i
ng
commit
|
commitdiff
|
tree
2018-03-14
Mark Abrah
a
m
Make
a
p
ers
i
s
tent
p
hysi
c
a
l
node co
m
m
u
ni
c
ator
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fix mdrun s
i
gnalling with
AWH bias s
h
arin
g
commit
|
commitdiff
|
tree
2018-03-13
B
erk Hess
Add
AWH fixe
s
to release notes
commit
|
commitdiff
|
tree
2018-03-13
Szilárd P
á
ll
Re
q
uire OpenCL 1
.
2
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH e
n
s
emble check
p
ointing
commit
|
commitdiff
|
tree
2018-03-13
Berk Hes
s
Fix AWH de
c
onvol
u
tion when shari
n
g a bias
commit
|
commitdiff
|
tree
2018-03-13
Mark Abraham
Introduc
e
const
r
ain_shak
e
commit
|
commitdiff
|
tree
2018-03-13
S
zilárd
Páll
Fix
cla
n
g 6
.
0 with CUD
A
9
.
0
commit
|
commitdiff
|
tree
2018-03-13
Mark Abraham
M
e
rge "
M
erge
branch release
-
2018
"
commit
|
commitdiff
|
tree
2018-03-09
B
erk Hess
Correct
p
db2gmx -missing option
commit
|
commitdiff
|
tree
2018-03-06
Ber
k
Hess
Convert t_f
i
lenm
to C
+
+
commit
|
commitdiff
|
tree
2018-03-06
M
a
rk Abraha
m
Merge bran
c
h releas
e
-2018
commit
|
commitdiff
|
tree
2018-03-06
Mark Abraham
Fixed
dvdlamb
d
a for SHAKE + F
E
commit
|
commitdiff
|
tree
2018-03-05
Szilárd Páll
A
dd to the contributor section
commit
|
commitdiff
|
tree
2018-03-01
Berk Hes
s
D
e
t
ect AMD
SMT topology
commit
|
commitdiff
|
tree
2018-02-28
M
ark Abrah
a
m
Moved and
removed co
n
str
a
i
n
t
code
commit
|
commitdiff
|
tree
2018-02-28
M
a
rk Abraham
Reorganiz
e
d constraint code
commit
|
commitdiff
|
tree
2018-02-27
Mark Abra
h
am
Fix GPU uti
l
s test
commit
|
commitdiff
|
tree
2018-02-26
Paul
B
auer
Chang
e
T
NG file o
p
ening
commit
|
commitdiff
|
tree
2018-02-26
Mark Abraham
Permit define
.
mdp field to assign values
commit
|
commitdiff
|
tree
2018-02-26
Aleksei
I
u
p
inov
Advice u
s
e
r
s on
i
nf
i
nite output
o
f
T
P
I
commit
|
commitdiff
|
tree
2018-02-26
Mark Abrah
a
m
Organ
i
ze
f
or recording 2016-era re
l
ease no
t
es and add
.
.
.
commit
|
commitdiff
|
tree
2018-02-23
B
e
rk Hess
Fix
md integrator with Nose
-
Hoover coupling
commit
|
commitdiff
|
tree
2018-02-21
M
ar
k
Ab
r
aham
Enhance
d
do
c
s of p
i
mpl
p
ointe
r
h
elper
commit
|
commitdiff
|
tree
2018-02-16
Mark Abra
h
am
M
e
rge branch release-2016 into
r
ele
a
se-2018
commit
|
commitdiff
|
tree
2018-02-16
Mark Abraha
m
Bumped patch v
e
rsion for next rel
e
ase
commit
|
commitdiff
|
tree
2018-02-16
B
e
rk He
s
s
Correct multisim MP
I
barrier
commit
|
commitdiff
|
tree
2018-02-16
Mark
Abraham
M
e
rge
branch release-2018 into
m
a
s
ter
commit
|
commitdiff
|
tree
2018-02-16
Mark Abraham
Ver
s
ion 201
6
.
5
commit
|
commitdiff
|
tree
2018-02-15
Mark Abra
h
am
Use struct for checkpoint header content
s
commit
|
commitdiff
|
tree
2018-02-15
Ale
k
sei Iupinov
Update FFTW
b
uild
t
o 3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-14
Mark
Abraham
R
emove r
e
ad_
c
heckpoint_st
a
te
commit
|
commitdiff
|
tree
2018-02-14
Berk H
e
ss
Re
m
o
v
e
s
u
pport for tpx version before 58/g
m
x4
.
0
commit
|
commitdiff
|
tree
2018-02-14
Mark Abraha
m
Use std::vector
for checkpoin
t
output
f
iles
commit
|
commitdiff
|
tree
2018-02-14
Mark
Abraham
M
e
rge
branch
re
l
ease-2016 into release-2018
commit
|
commitdiff
|
tree
2018-02-14
Berk H
e
ss
Fix r
a
nge bug in
add
_
selection_g
r
oups in tngio
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
Aleksei Iup
i
nov
Re
p
l
a
ce t
h
e
r
emaining EXPECT
_
DEATH with E
X
PECT_DE
A
T
H_IF_
S
UPP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
Alek
s
ei
I
upin
o
v
Add Devi
c
eBuffer as
a
typedef for cl_mem/
d
ev
i
c
e
pon
t
er
commit
|
commitdiff
|
tree
2018-02-14
Szilárd Páll
R
emov
e
b
a
rriers
prevent
i
n
g
tex
t
ur
e
refer
e
nce
r
aces
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix grompp
n
et ch
a
rge check
commit
|
commitdiff
|
tree
2018-02-14
Berk Hes
s
F
i
x
grompp net charge
c
heck
commit
|
commitdiff
|
tree
2018-02-14
Mark Ab
r
aha
m
Prepare
release notes for
2
01
8
.
1
commit
|
commitdiff
|
tree
2018-02-13
M
a
rk Abr
a
ha
m
Use death test only wh
e
n su
p
por
t
ed
commit
|
commitdiff
|
tree
2018-02-13
Mark Abraham
S
e
para
t
e multisim f
r
om commrec
commit
|
commitdiff
|
tree
2018-02-12
M
a
rk
A
br
a
ham
Analyse
threa
d
s on
node be
f
ore
s
et
t
ing af
f
inities
commit
|
commitdiff
|
tree
2018-02-12
Mark Abraham
Fi
x
r
e
a
ding old forc
e
fi
e
ld files
commit
|
commitdiff
|
tree
2018-02-09
Mark Abraham
Merge br
a
n
ch release-2018
commit
|
commitdiff
|
tree
2018-02-08
Mark A
b
raham
Merg
e
"Merge branch rele
a
se-201
6
int
o
re
l
ease-20
1
8
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Ma
r
k Abrah
a
m
Merge branc
h
relea
s
e
-
2016 into release
-
2
018
commit
|
commitdiff
|
tree
2018-02-08
Aleks
e
i Iupin
o
v
Ena
b
le debug FP e
x
ceptions without T
P
I, not with TPI
commit
|
commitdiff
|
tree
2018-02-08
Mark Abr
a
ham
Me
r
ge "Merge branch
'
r
eleas
e
-2018' into mas
t
er
"
commit
|
commitdiff
|
tree
2018-02-06
Mark Abraham
Preve
n
t log file
energy aver
a
ge
p
rinti
n
g
d
iv
i
ding by
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
Aleksei Iupinov
Don't print impos
s
ible CUDA
v
e
r
sion
n
umbers in
absence
.
.
.
commit
|
commitdiff
|
tree
2018-02-01
Paul Bau
e
r
Add inform
a
tion for
n
2t file format
commit
|
commitdiff
|
tree
2018-01-27
Mark A
b
r
a
ham
Re
m
o
v
e unuse
d
declara
t
ion
commit
|
commitdiff
|
tree
next