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Partial conversion of gmx_domdec_t to C++
2018-06-13
M
a
r
k
Ab
r
aham
Bump lmfit support to
version 7
commit
|
commitdiff
|
tree
2018-06-12
Mark A
b
raham
Prepare for GROMACS 2019 release n
o
tes
commit
|
commitdiff
|
tree
2018-06-06
M
a
rk Abraham
Move IMD initialization and fuse D
D
setup
commit
|
commitdiff
|
tree
2018-06-05
Mark A
b
raham
Make proper BoxDeformat
i
on class
commit
|
commitdiff
|
tree
2018-06-05
Mar
k
Abr
a
ham
Separate flexibl
e
constrai
n
t count
i
ng
commit
|
commitdiff
|
tree
2018-06-05
M
a
rk A
b
rah
a
m
Make Constraint
s
a p
r
o
per cl
a
ss
commit
|
commitdiff
|
tree
2018-06-04
M
a
rk Abraham
Update Awh initialization and lifetime managem
e
nt
commit
|
commitdiff
|
tree
2018-06-04
Ma
r
k Abraham
Remove re
d
undant shell-code fatal e
r
r
o
rs
commit
|
commitdiff
|
tree
2018-05-25
Mark Abraham
C
le
a
n up force
.
h
a
nd its use
commit
|
commitdiff
|
tree
2018-05-24
Mar
k
Abraha
m
Remove
b
Do
m
Dec from t_forcerec
commit
|
commitdiff
|
tree
2018-05-24
Mark Abraham
M
ove respon
s
ib
i
lity for bonde
d
t
h
re
a
ding
decomposition
commit
|
commitdiff
|
tree
2018-05-24
Mark Abrah
a
m
Relocate
GPU initialization
f
o
r
PM
E
commit
|
commitdiff
|
tree
2018-05-24
Mark Abr
a
ham
Reform Ewa
l
d-module cmake handlin
g
commit
|
commitdiff
|
tree
2018-05-23
Mark
Abr
a
ham
Clean up PME testing
commit
|
commitdiff
|
tree
2018-05-04
Mar
k
Abraham
Merge "Merge
b
r
anch
relea
s
e-2018"
commit
|
commitdiff
|
tree
2018-05-04
Mark A
b
raham
More
const
c
orrectnes
s
commit
|
commitdiff
|
tree
2018-05-03
M
a
rk
Abraham
Merge branch release-2
0
18
commit
|
commitdiff
|
tree
2018-04-26
Mark Abraham
Revert "Tweak
PME
r
un
m
ode
c
hecks"
commit
|
commitdiff
|
tree
2018-04-25
Mark Abra
h
am
Refact
o
r SD upda
t
e
commit
|
commitdiff
|
tree
2018-04-18
Ma
r
k
Abraha
m
I
n
t
r
oduce
gm
x
_use
d
_i
n
_de
b
ug
commit
|
commitdiff
|
tree
2018-04-17
M
ar
k
Abraham
Shift per-s
t
ep c
o
ntrol
logi
c
to d
o
_md
commit
|
commitdiff
|
tree
2018-04-17
Mark
A
b
r
aham
Break
a
part update_con
s
t
r
ai
n
ts
commit
|
commitdiff
|
tree
2018-04-16
Mark Abraham
Updated mdrun comparison infrastructu
r
e
commit
|
commitdiff
|
tree
2018-04-13
Mark Abraham
Me
r
ge branch release-20
1
8
commit
|
commitdiff
|
tree
2018-04-13
Mar
k
Abr
a
ham
Clean up const
r
aints code
commit
|
commitdiff
|
tree
2018-04-12
M
ark
A
b
raha
m
Re
m
ove use o
f
where(
)
, if DE
B
UG etc
.
commit
|
commitdiff
|
tree
2018-04-12
M
ark Abraham
R
eorgani
z
e e
n
er
g
y
e
valuation
for EM
commit
|
commitdiff
|
tree
2018-04-05
M
ark Abr
a
ham
Simpli
f
ied handling of
s
i
mulation
r
unners
commit
|
commitdiff
|
tree
2018-04-05
Mark Abraham
C
rea
t
e g
r
omac
s
/mdrun mo
d
ul
e
and move code ther
e
commit
|
commitdiff
|
tree
2018-04-04
Mark Abraham
Quiet
c
heckpoint reading
commit
|
commitdiff
|
tree
2018-04-03
M
ark Abra
h
am
Remo
v
e left
o
ver
mention of t
w
i
n-rang
e
scheme
commit
|
commitdiff
|
tree
2018-04-03
Ma
r
k Ab
r
aham
Merge "Merge bra
n
ch
release-
2
018"
commit
|
commitdiff
|
tree
2018-03-28
Mark Abraham
F
r
ee mor
e
m
e
mory i
n
g
r
ompp
a
nd mdrun
commit
|
commitdiff
|
tree
2018-03-28
Mar
k
Abraham
M
e
rge branc
h
release-2018
commit
|
commitdiff
|
tree
2018-03-27
Mar
k
Abraham
Clarified mdp o
p
tions relating to bonds
commit
|
commitdiff
|
tree
2018-03-27
M
ark
Ab
r
aham
M
ore gcc-8 fixes fo
r
P
OWE
R
commit
|
commitdiff
|
tree
2018-03-22
Mark
A
braha
m
U
pd
a
ted to
pr
e
pare fo
r
2018
.
2 r
e
l
e
ase
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
Version
2
018
.
1
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraha
m
Merge "Me
r
ge branch release-201
6
into release-
2
018
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
M
ark
A
b
raham
U
p
date re
l
eas
e
notes
for 2018
.
1
commit
|
commitdiff
|
tree
2018-03-20
Ma
r
k Abraham
M
erge
b
ranch releas
e
-2016 in
t
o relea
s
e-
2
018
commit
|
commitdiff
|
tree
2018-03-20
Mark Abr
a
ham
Update use
of
g
pu_id
i
n
Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
U
p
da
t
e use of gpu_id in
J
e
nkins
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Upd
a
te use o
f
g
p
u_id
i
n
Jenk
i
ns
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraha
m
Add help
e
r f
u
nction to
make a vector from an A
r
rayRef
commit
|
commitdiff
|
tree
2018-03-19
Ma
r
k Abraham
Fix VS
X
S
I
MD wi
t
h gcc 8
commit
|
commitdiff
|
tree
2018-03-14
Mark Abraham
Make a p
e
rs
i
stent physical node communic
a
tor
commit
|
commitdiff
|
tree
2018-03-13
Mark Abrah
a
m
Add more c
o
n
s
t to uses
of
t
_commrec and t_inpu
t
rec
commit
|
commitdiff
|
tree
2018-03-13
Mark
Abraha
m
Introdu
c
e constr
a
in_shake
commit
|
commitdiff
|
tree
2018-03-13
Mark
A
braham
M
erge
"Merge branch release-2018"
commit
|
commitdiff
|
tree
2018-03-12
Ma
r
k A
b
raham
Test gcc-6 and cud
a
-
9
.
0
commit
|
commitdiff
|
tree
2018-03-06
Mark Abraham
Merge branch r
e
lease-2018
commit
|
commitdiff
|
tree
2018-03-06
Ma
r
k Ab
r
a
ham
Fixed
d
vdlambda
for SHA
K
E + FE
commit
|
commitdiff
|
tree
2018-02-28
Ma
r
k Abrah
a
m
Move
d
and removed constraint
code
commit
|
commitdiff
|
tree
2018-02-28
Mar
k
Abraham
Reorganize
d
co
n
strain
t
code
commit
|
commitdiff
|
tree
2018-02-27
M
ark
Abraham
F
i
x
G
PU
utils test
commit
|
commitdiff
|
tree
2018-02-26
Mark Abraham
P
ermit define
.
mdp field to assi
g
n values
commit
|
commitdiff
|
tree
2018-02-26
M
a
rk Abr
a
ham
Organize for r
e
co
r
ding 201
6
-era r
e
lease notes and add
.
.
.
commit
|
commitdiff
|
tree
2018-02-21
Mar
k
A
braham
Enhanced docs of pi
m
pl pointer helper
commit
|
commitdiff
|
tree
2018-02-19
Mark Abr
a
ham
Remove cycl
e
s
u
pp
r
e
s
si
o
n
commit
|
commitdiff
|
tree
2018-02-19
Mark Abraham
Dis
a
llowed
chan
g
e
of
e
nsemble f
o
r
checkpo
i
nt restart
commit
|
commitdiff
|
tree
2018-02-16
M
a
r
k
A
b
raham
Mer
g
e branch release-2016 into release-2018
commit
|
commitdiff
|
tree
2018-02-16
Mar
k
Abr
a
ham
Bumped
p
atch
v
ersion for ne
x
t rele
a
se
commit
|
commitdiff
|
tree
2018-02-16
Ma
r
k Abraham
M
e
rge
branch rel
e
a
se-
2
018
into ma
s
t
er
commit
|
commitdiff
|
tree
2018-02-16
Mark
A
b
r
a
ha
m
Version 20
1
6
.
5
commit
|
commitdiff
|
tree
2018-02-15
M
ar
k
Abra
h
am
Use str
u
ct for checkpoint
h
eade
r
contents
commit
|
commitdiff
|
tree
2018-02-14
Mark Abraha
m
R
e
m
ove read_che
c
k
point_
s
tate
commit
|
commitdiff
|
tree
2018-02-14
Mark Abraham
U
se
std::vecto
r
for checkpoint outputfiles
commit
|
commitdiff
|
tree
2018-02-14
Mark Ab
r
a
h
am
M
e
rge branch release-2016 into re
l
e
a
se-
2
0
1
8
commit
|
commitdiff
|
tree
2018-02-14
Mark Abra
h
am
F
i
x bug in ch
e
ckpoi
n
t error checki
n
g
commit
|
commitdiff
|
tree
2018-02-14
Mark
A
braha
m
Prep
a
re releas
e
notes
f
or
2
018
.
1
commit
|
commitdiff
|
tree
2018-02-13
M
a
rk Abraham
Use death test only when support
e
d
commit
|
commitdiff
|
tree
2018-02-13
Mark Abraham
Sepa
r
ate mult
i
sim fr
o
m co
m
mrec
commit
|
commitdiff
|
tree
2018-02-12
Mark Abraham
Remove c
o
m
m
rec from hardware de
t
ection
commit
|
commitdiff
|
tree
2018-02-12
Mark
A
braham
A
nalyse
t
hre
a
ds o
n
node
before setting
a
ffinities
commit
|
commitdiff
|
tree
2018-02-12
Mark Abrah
a
m
Fix
reading old for
c
e field files
commit
|
commitdiff
|
tree
2018-02-09
Mark A
b
raham
Merge br
a
nch r
e
lease-20
1
8
commit
|
commitdiff
|
tree
2018-02-08
Mark
A
brah
a
m
U
s
e
more portable
p
y
thon shebangs
commit
|
commitdiff
|
tree
2018-02-08
M
ark Abraham
Merge "Merge branch release-2016 into release-2018
.
.
.
commit
|
commitdiff
|
tree
2018-02-08
M
ark Abraham
Mer
g
e bra
n
ch release-
2
0
1
6 into r
e
lease-2018
commit
|
commitdiff
|
tree
2018-02-08
Mark Abraham
M
erge "
M
erge bran
c
h 'release
-
2018' into master"
commit
|
commitdiff
|
tree
2018-02-06
Mark
A
braham
Prevent
l
og file energy
av
e
rage pri
n
t
ing
di
v
iding by
.
.
.
commit
|
commitdiff
|
tree
2018-02-06
Mark Abraham
U
s
e isf
i
nite unambiguously
commit
|
commitdiff
|
tree
2018-01-30
M
a
r
k Abr
a
ham
Replac
e
macros for mu
l
ti-sim
commit
|
commitdiff
|
tree
2018-01-30
Mark
Abr
a
ham
Update GoogleTest to 1
.
8
.
0
commit
|
commitdiff
|
tree
2018-01-27
Ma
r
k Abraham
Remove
u
nused declaration
commit
|
commitdiff
|
tree
2018-01-25
Ma
r
k Ab
r
a
ham
Remove
unused
f
i
elds of t_
c
ommrec
commit
|
commitdiff
|
tree
2018-01-25
Mark Abra
h
am
Reduced i
n
clude
s
of common headers in heade
r
s
commit
|
commitdiff
|
tree
2018-01-25
M
ark Abra
h
am
Remo
v
ed mdrun -multi
commit
|
commitdiff
|
tree
2018-01-24
M
ark Abraham
Chang
e
mul
t
i
-sim tests to use -multid
i
r
commit
|
commitdiff
|
tree
2018-01-24
Mark
A
b
raham
Remove gm
x
_
inline
commit
|
commitdiff
|
tree
2018-01-24
Mark
A
b
raham
Teach include sort
e
r to ignore cmak
e
-test
fil
e
s
commit
|
commitdiff
|
tree
2018-01-24
Mark Abraham
Move Wi
n
dows
i
cc config to p
o
st-su
b
mit te
s
ting
commit
|
commitdiff
|
tree
2018-01-24
Mark Ab
r
a
h
am
R
e
p
l
ace gmx_bo
o
l w
i
th bool
i
n b
i
tma
s
k functions
commit
|
commitdiff
|
tree
2018-01-23
M
ark
A
braha
m
Remove supp
o
rt for
implicit so
l
vation
commit
|
commitdiff
|
tree
2018-01-23
Mark Abraham
Remove topol
o
gy support for
i
mplic
i
t solvation
commit
|
commitdiff
|
tree
2018-01-23
M
ark Abraham
P
reliminary cleanup before removin
g
ifdef cpluspl
u
s
commit
|
commitdiff
|
tree
2018-01-19
Mark Abraham
Merge "Me
r
g
e
branch '
r
elease-2018' in
t
o
m
ast
e
r"
commit
|
commitdiff
|
tree
2018-01-19
Mark Abr
a
ham
A
d
d dev-guide
d
ocs for au
t
o
m
a
t
ic update o
f
re
g
ressiont
e
sts
commit
|
commitdiff
|
tree
2018-01-19
Mark Abraham
Fixes
f
or issues found b
y
c
l
ang 6
commit
|
commitdiff
|
tree
next