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Move natoms_mol out of gmx_molblock_t
2018-04-16
Be
r
k Hess
Move
natoms_m
o
l ou
t
of gmx_m
o
lblock_t
commit
|
commitdiff
|
tree
2018-04-16
Mark
Abraham
Up
d
ated mdrun
c
ompari
s
on i
n
fr
a
struct
u
r
e
commit
|
commitdiff
|
tree
2018-04-13
Mark Ab
r
aham
Clean up
co
n
s
t
r
a
ints co
d
e
commit
|
commitdiff
|
tree
2018-04-12
Mark
A
braha
m
R
emo
v
e use of where(),
i
f DEBUG etc
.
commit
|
commitdiff
|
tree
2018-04-12
Mar
k
Abraham
Reorgan
i
ze
ene
r
gy e
v
a
l
uation for E
M
commit
|
commitdiff
|
tree
2018-04-10
Aleksei
I
upinov
Prevent OpenCL timin
g
m
emory lea
k
commit
|
commitdiff
|
tree
2018-04-09
Berk He
s
s
C
onv
e
rt gmx_molblock
_
t
t
o C+
+
commit
|
commitdiff
|
tree
2018-04-05
Ma
r
k Abraham
Simplified handling of simul
a
tion run
n
ers
commit
|
commitdiff
|
tree
2018-04-05
Mark Abra
h
a
m
Create gro
m
acs/mdrun mod
u
le and move code ther
e
commit
|
commitdiff
|
tree
2018-04-05
Szil
á
rd
P
áll
Ref
a
ctor cj p
r
eload in the nonbonded
O
penCL ker
n
els
commit
|
commitdiff
|
tree
2018-04-04
M
a
rk
A
b
r
aham
Qui
e
t checkpoint reading
commit
|
commitdiff
|
tree
2018-04-04
Pascal Merz
Move
checkNumberOfBondedIn
t
eracti
o
ns
commit
|
commitdiff
|
tree
2018-04-03
Berk H
e
ss
Convert g
m
x_mtop_t to C++
commit
|
commitdiff
|
tree
2018-04-03
Mark Abraham
Remove leftover
m
e
ntion
of tw
i
n-r
a
nge sche
m
e
commit
|
commitdiff
|
tree
2018-04-03
M
ark
A
braham
Mer
g
e
"M
e
rge branch r
e
l
eas
e
-2018
"
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Mo
v
e file opening ou
t
of init_pull()
commit
|
commitdiff
|
tree
2018-03-29
Szilár
d
Páll
Twe
a
k/enab
l
e icc 18 post-sub
m
it
tests
commit
|
commitdiff
|
tree
2018-03-29
Mag
n
us
Lundborg
Improved check of if
only forces a
r
e c
o
mp
u
ted in
do
_
pair
s
()
commit
|
commitdiff
|
tree
2018-03-29
Paul Bau
e
r
Fi
x
cmake
Sphinx detect
i
on for ver
s
ions
>
1
.
6
.
4
commit
|
commitdiff
|
tree
2018-03-29
S
z
ilárd Páll
Switch
CUDA
9
.
0
/g
c
c 5 test
to CUDA 9
.
1/gcc 6
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Modularize pul
l
_coord_
w
ork_t
commit
|
commitdiff
|
tree
2018-03-28
M
a
rk Ab
r
aham
Fre
e
more memor
y
in grom
p
p an
d
mdrun
commit
|
commitdiff
|
tree
2018-03-28
Berk Hess
Remove
m
ols from gmx_mtop_t
commit
|
commitdiff
|
tree
2018-03-28
Ma
r
k Abraham
Merge
branch release
-
20
1
8
commit
|
commitdiff
|
tree
2018-03-27
M
ark Abraham
Clarified mdp op
t
io
n
s
r
e
l
a
t
ing
t
o bonds
commit
|
commitdiff
|
tree
2018-03-27
M
a
r
k Abraha
m
More gcc-
8
fixes for POW
E
R
commit
|
commitdiff
|
tree
2018-03-21
D
a
vid van der Spoel
Re
n
amed ent
r
o
p
y
.
* to thermochemi
s
try
.
*
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
Version 201
8
.
1
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
M
e
rge "Merge br
a
n
c
h release-
2
0
1
6 in
t
o
release-
2
018
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
Mar
k
Abraham
U
pda
t
e
r
elease
notes
for 2018
.
1
commit
|
commitdiff
|
tree
2018-03-20
M
ark Abrah
a
m
Merge branch release
-
2016 into
r
e
l
ease-2018
commit
|
commitdiff
|
tree
2018-03-20
M
ark A
b
raham
U
p
date use of gpu_id i
n
Jenki
n
s
commit
|
commitdiff
|
tree
2018-03-20
Ber
k
Hess
Disa
l
low single simulation with multisim
commit
|
commitdiff
|
tree
2018-03-20
Ma
r
k Abraham
U
p
da
t
e
u
se of g
p
u_i
d
in Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Mark Ab
r
aham
U
p
dat
e
use
of
g
pu_id in
Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Add
h
e
l
p
e
r functi
o
n
to ma
k
e
a vector from
an Arra
y
R
ef
commit
|
commitdiff
|
tree
2018-03-19
Mark A
b
r
a
h
am
Fix VSX SIMD with gcc 8
commit
|
commitdiff
|
tree
2018-03-16
Pa
u
l Baue
r
Only free top
o
lo
g
y whe
n
allo
c
ated
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
Corr
e
ct PMF sign error in AWH bias sharing
commit
|
commitdiff
|
tree
2018-03-14
B
erk
Hess
I
m
pr
o
ve i
n
ter-sim
u
lation signali
n
g
commit
|
commitdiff
|
tree
2018-03-14
Mark Abraham
M
ake a persistent physic
a
l
nod
e
communica
t
or
commit
|
commitdiff
|
tree
2018-03-14
Berk
H
e
ss
Fix mdr
u
n
signallin
g
with AWH bia
s
sharing
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Add AW
H
fixes
t
o
re
l
ease notes
commit
|
commitdiff
|
tree
2018-03-13
Szilár
d
Páll
Req
u
ire OpenCL 1
.
2
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH
e
ns
e
mble che
c
k
p
o
inting
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH
d
e
convo
l
ution when sh
a
r
i
ng
a
bias
commit
|
commitdiff
|
tree
2018-03-13
M
a
rk Abraham
I
ntro
d
u
c
e
c
onstrai
n
_shake
commit
|
commitdiff
|
tree
2018-03-13
Szilárd
P
á
ll
Fi
x
clang 6
.
0 with
C
UDA 9
.
0
commit
|
commitdiff
|
tree
2018-03-13
Mark Abra
h
am
Merge "Merge br
a
nch release-2018
"
commit
|
commitdiff
|
tree
2018-03-09
Be
r
k Hes
s
Correct pdb2gmx -missing op
t
ion
commit
|
commitdiff
|
tree
2018-03-06
Berk Hess
Conve
r
t t_f
i
lenm t
o
C++
commit
|
commitdiff
|
tree
2018-03-06
Ma
r
k
Abrah
a
m
Me
r
ge branch rel
e
ase-2018
commit
|
commitdiff
|
tree
2018-03-06
Mark Abraham
F
ixed
d
vdlambda
f
or
S
H
A
KE + F
E
commit
|
commitdiff
|
tree
2018-03-05
Szil
á
rd P
á
ll
Add to the co
n
tribu
t
or
s
ection
commit
|
commitdiff
|
tree
2018-03-01
Berk
H
ess
Det
e
c
t
AMD SMT topology
commit
|
commitdiff
|
tree
2018-02-28
Mark Ab
r
a
ham
Move
d
a
nd
r
emoved c
o
nstraint cod
e
commit
|
commitdiff
|
tree
2018-02-28
Ma
r
k Abraham
Reorg
a
n
ized con
s
traint
c
o
d
e
commit
|
commitdiff
|
tree
2018-02-27
Mark
A
b
raham
Fix GPU utils test
commit
|
commitdiff
|
tree
2018-02-26
Pa
u
l Bauer
Change TNG file openi
n
g
commit
|
commitdiff
|
tree
2018-02-26
Mar
k
Abraham
Permit
d
efi
n
e
.
mdp
f
ield to assi
g
n values
commit
|
commitdiff
|
tree
2018-02-26
Aleksei Iupinov
Advice users on
infinite output of TPI
commit
|
commitdiff
|
tree
2018-02-26
Mark Abraham
Organize
f
o
r
recording 2016-
e
ra rel
e
ase no
t
es and add
.
.
.
commit
|
commitdiff
|
tree
2018-02-23
Berk Hess
Fix md inte
g
rato
r
with No
s
e-Hoover coupling
commit
|
commitdiff
|
tree
2018-02-21
Mark Abraham
Enhanc
e
d docs of pimpl pointer helper
commit
|
commitdiff
|
tree
2018-02-16
Mar
k
A
braham
Me
r
ge branch
r
elease-201
6
in
t
o r
e
l
e
ase-2018
commit
|
commitdiff
|
tree
2018-02-16
Mark A
b
rah
a
m
B
umped pa
t
ch version for next r
e
lea
s
e
commit
|
commitdiff
|
tree
2018-02-16
Be
r
k
Hes
s
Correct multisim MPI barrier
commit
|
commitdiff
|
tree
2018-02-16
Mark Abr
a
ham
Mer
g
e bran
c
h
release-2
0
18 into ma
s
ter
commit
|
commitdiff
|
tree
2018-02-16
Mark Abraham
Vers
i
on 2016
.
5
commit
|
commitdiff
|
tree
2018-02-15
M
a
r
k
Abraham
U
se struct f
o
r
c
h
e
ckpoint hea
d
er contents
commit
|
commitdiff
|
tree
2018-02-15
Alekse
i
Iupinov
Update
FFTW build to 3
.
3
.
7
commit
|
commitdiff
|
tree
2018-02-14
Mark A
b
r
a
ham
Remove read_checkpoint_st
a
te
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Remov
e
suppor
t
for tpx ver
s
ion
before
58/g
m
x4
.
0
commit
|
commitdiff
|
tree
2018-02-14
Mark
Abraham
U
se std::vecto
r
for
checkpoint outputfiles
commit
|
commitdiff
|
tree
2018-02-14
M
ark
A
braham
Mer
g
e b
r
anch rele
a
se-2016 into
r
el
e
ase-20
1
8
commit
|
commitdiff
|
tree
2018-02-14
Berk He
s
s
Fix
r
an
g
e bu
g
in add
_
s
e
lection_
g
roups
in tngio
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
A
l
e
ks
e
i
I
upin
o
v
Re
p
lac
e
the r
e
maining EXP
E
CT_DEATH
with EXPECT_
D
EA
T
H
_
IF_SUPP
.
.
.
commit
|
commitdiff
|
tree
2018-02-14
Aleksei Iupino
v
Add D
e
viceBuffer a
s
a typede
f
for cl_mem/devic
e
ponter
commit
|
commitdiff
|
tree
2018-02-14
Szilá
r
d
P
áll
Re
m
o
v
e barri
e
rs preve
n
tin
g
text
u
re r
e
ference races
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix grompp net charge che
c
k
commit
|
commitdiff
|
tree
2018-02-14
Be
r
k Hess
Fix gr
o
m
pp net
c
harge c
h
e
ck
commit
|
commitdiff
|
tree
2018-02-14
M
a
rk Ab
r
aham
Prepa
r
e r
e
lease notes for 2
0
18
.
1
commit
|
commitdiff
|
tree
2018-02-13
M
a
r
k Abrah
a
m
Use death test
o
n
ly w
h
e
n
supp
o
rted
commit
|
commitdiff
|
tree
2018-02-13
Mark Abraham
S
e
parate multisim f
r
om c
o
mmrec
commit
|
commitdiff
|
tree
2018-02-12
M
a
r
k
A
b
r
aham
Analy
s
e threads on node before setting
a
ff
i
nities
commit
|
commitdiff
|
tree
2018-02-12
Mark Abraham
Fix reading ol
d
force f
i
eld f
i
les
commit
|
commitdiff
|
tree
2018-02-09
Mark Abr
a
ham
Merge branch release-2018
commit
|
commitdiff
|
tree
2018-02-08
Mark Abraham
Merge "Merge branch rele
a
se-2016 int
o
release-2018
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
Mark Abraham
Merg
e
b
r
anch release-2016 into releas
e
-2018
commit
|
commitdiff
|
tree
2018-02-08
Al
e
ksei Iupino
v
Enable debug FP except
i
ons without
TPI, not with TPI
commit
|
commitdiff
|
tree
2018-02-08
Ma
r
k Ab
r
aham
Merge
"
Merge bran
c
h 'release-2018' i
n
t
o
m
ast
e
r"
commit
|
commitdiff
|
tree
2018-02-06
M
a
rk A
b
ra
h
am
Preven
t
log
file energy av
e
rag
e
printi
n
g divid
i
ng
by
.
.
.
commit
|
commitdiff
|
tree
2018-02-02
A
l
eksei
I
upinov
Don't print
i
m
possible CU
D
A version numb
e
rs in absence
.
.
.
commit
|
commitdiff
|
tree
2018-02-01
Paul Bauer
Add information for n2t file format
commit
|
commitdiff
|
tree
2018-01-27
Mark A
b
raham
Remove
u
nu
s
ed declaration
commit
|
commitdiff
|
tree
2018-01-25
Mark Abraham
Remove unused fi
e
l
d
s of t_commr
e
c
commit
|
commitdiff
|
tree
2018-01-25
Mark Abraham
Reduced includes of c
o
mmon
h
eaders
i
n headers
commit
|
commitdiff
|
tree
2018-01-25
Ma
r
k Abraham
Removed mdrun
-
multi
commit
|
commitdiff
|
tree
2018-01-24
Mark Abraham
Change
m
u
lti
-
sim tests to use
-
multi
d
i
r
commit
|
commitdiff
|
tree
2018-01-24
Ma
r
k Abraham
Remove gmx_inline
commit
|
commitdiff
|
tree
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