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Add integration tests for exact restarts
2019-06-30
Szilárd Páll
Cr
e
ate dedicat
e
d subcounter for
no
n
b
o
nded FEP
commit
|
commitdiff
|
tree
2019-06-30
K
evin
B
oy
d
R
e
mo
v
e group
scheme checks from runner
commit
|
commitdiff
|
tree
2019-06-30
Magnus Lundborg
Cleaning up
t
he GPU bonde
d
kernel
commit
|
commitdiff
|
tree
2019-06-20
Paul Bauer
Use ISeri
a
li
z
er fo
r
T
P
R
file IO
commit
|
commitdiff
|
tree
2019-06-20
B
erk Hess
Templa
t
e free-
e
nergy kernel on soft-co
r
e
commit
|
commitdiff
|
tree
2019-06-20
Christi
a
n Blau
Add Bas
i
c
Vect
o
r
s
caling, max, mi
n
and toIvec
commit
|
commitdiff
|
tree
2019-06-19
Szilárd Pá
l
l
Disab
l
e PME GPU on App
l
e
O
p
e
nCL
commit
|
commitdiff
|
tree
2019-06-19
Berk Hess
Re
f
actor PM
E
atom han
d
ling
commit
|
commitdiff
|
tree
2019-06-19
Paul Bauer
S
plit tpr
h
e
ade
r
reading re
a
ding
from
t
pr
b
ody
commit
|
commitdiff
|
tree
2019-06-19
Berk He
s
s
Removed
u
nused code p
a
ths
i
n the NB FE kernel
commit
|
commitdiff
|
tree
2019-06-18
Paul Bauer
Fix
gmx dump
commit
|
commitdiff
|
tree
2019-06-18
M
a
rk Ab
r
aham
Move c
o
de
h
a
n
dling m
d
run -gp
u
_id to taskassignment
.
.
.
commit
|
commitdiff
|
tree
2019-06-18
Berk
Hess
M
a
ke forc
e
rec const in dispa
t
c
h
Nonbond
e
dKernel()
commit
|
commitdiff
|
tree
2019-06-18
Chr
i
stian Blau
Mr
c
fo
r
mat header
to
l
at
t
ic
e
coordinate t
r
ansform
commit
|
commitdiff
|
tree
2019-06-18
C
hristian Blau
Density si
m
ilarity measure
a
nd gradient
commit
|
commitdiff
|
tree
2019-06-18
M
.
E
r
ic Ir
r
gang
Reduce docker image
size for gmxapi CI
.
commit
|
commitdiff
|
tree
2019-06-18
Artem Zhmurov
Bug
fix: Cons
t
raints tests are not instantiat
e
d with
.
.
.
commit
|
commitdiff
|
tree
2019-06-12
Mark
A
braham
Fix p
y
g
ments detection fo
r
s
ph
i
nx for
docs bu
i
ld
commit
|
commitdiff
|
tree
2019-06-11
Ma
r
k Abraham
Us
e
RAII
app
r
oac
h
es for hardware information d
e
t
e
ction
commit
|
commitdiff
|
tree
2019-06-11
Mark Abraham
Clean up
m
ultisim, com
m
unic
a
tion, and REM
D
code
commit
|
commitdiff
|
tree
2019-06-11
Mark Abraham
In
i
tia
l
ize all of gm
x
_domdec_comm_t
commit
|
commitdiff
|
tree
2019-06-11
Pa
u
l
B
auer
F
i
x
res
i
d
u
e an
d
molecu
l
e ind
e
x
i
ng in
se
l
ections
commit
|
commitdiff
|
tree
2019-06-11
Ber
k
Hess
Allow AWH
g
eo
m
etr
y
'di
r
ection'
to be periodic
commit
|
commitdiff
|
tree
2019-06-11
Paul Bauer
Ad
d
che
c
k for too many grid
p
oin
t
s in hbon
d
commit
|
commitdiff
|
tree
2019-06-05
Be
r
k Hess
F
ix re
f
erence SIMD memory a
l
ignment
commit
|
commitdiff
|
tree
2019-05-29
Ber
k
Hess
Fix missing i
n
termolecula
r
interactions with DD
commit
|
commitdiff
|
tree
2019-05-29
S
z
i
l
á
r
d Páll
Template x
buf
f
er o
p
s
call on whether GPU is used
commit
|
commitdiff
|
tree
2019-05-27
P
a
scal Merz
Clean up
renamed
s
imul
a
tor
.
h file
commit
|
commitdiff
|
tree
2019-05-25
Pascal
M
e
r
z
Remove dependence of mdoutf_write_
t
o_traje
c
tory_files
.
.
.
commit
|
commitdiff
|
tree
2019-05-25
Pasca
l
Merz
Rename Integrator clas
s
commit
|
commitdiff
|
tree
2019-05-24
Artem Zhmurov
Clar
i
f
y
the EnergyOutput
I
II
commit
|
commitdiff
|
tree
2019-05-24
Artem
Z
h
murov
C
l
arif
y
t
he
E
ner
g
yOut
p
ut II
commit
|
commitdiff
|
tree
2019-05-24
Mark Abrah
a
m
Reor
d
er code befor
e
thread-MPI spawns t
h
reads
commit
|
commitdiff
|
tree
2019-05-23
Szilárd Páll
F
i
x mulit
p
le link refs in de
v
-ma
n
u
a
l
commit
|
commitdiff
|
tree
2019-05-23
M
ar
k
Abra
h
am
T
e
ach Ar
r
ayRefWithP
a
dding
t
o
make a cons
t
f
lavour
commit
|
commitdiff
|
tree
2019-05-23
B
erk H
e
s
s
F
ix
S
H
AKE dH/
d
lambda contributi
o
ns
commit
|
commitdiff
|
tree
2019-05-22
Mark Abr
a
ham
Rewrite starting
b
ehavior
commit
|
commitdiff
|
tree
2019-05-22
Ma
r
k Abraham
In
t
roduce
tri-st
a
te enums for resta
r
t
s
commit
|
commitdiff
|
tree
2019-05-22
Al
a
n
Gr
a
y
Pin X buffer wit
h
DD and use proper abstrac
t
ion i
n
.
.
.
commit
|
commitdiff
|
tree
2019-05-22
J
inke Fan
Add supp
o
rt for Hygon Dhyana processor
commit
|
commitdiff
|
tree
2019-05-22
Mark Abraham
Move fun
c
tionality to mdrunutility
commit
|
commitdiff
|
tree
2019-05-20
Mark Abr
a
ham
Fix equation typo
commit
|
commitdiff
|
tree
2019-05-16
Erik
L
indahl
Added more quotes
commit
|
commitdiff
|
tree
2019-05-14
Ma
r
k Abraham
Up
d
ate infras
t
ructure need
e
d
f
or restart rewrite
commit
|
commitdiff
|
tree
2019-05-10
Pau
l
B
a
u
er
Remove more manual memory m
a
nagement
commit
|
commitdiff
|
tree
2019-05-09
M
.
Er
i
c
Irrgang
More Python testing infra
s
tructu
r
e for gmxapi
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
E
r
ic Ir
r
gang
Add gmxapi
.
_log
g
ing submodul
e
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
Eric Irrgang
Upda
t
e I/O h
a
ndling in gmx
a
pi
.
commandline
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
E
ric
Irrgang
Expa
n
d g
m
x
a
pi
.
operation
t
ools to support
t
he dat
a
fl
o
w
.
.
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
Eric Irrgang
Fi
x
formatting and typos
.
commit
|
commitdiff
|
tree
2019-05-09
M
.
E
ric
I
rrgang
Suppo
r
t ba
s
i
c comman
d
lin
e
wrapp
e
r in gmxapi
commit
|
commitdiff
|
tree
2019-05-07
Mark Abraham
Add a
n
example of
u
sing an MPI wrapper compile
r
commit
|
commitdiff
|
tree
2019-05-03
M
a
rk Abraham
Mo
r
e test
s
for how mdrun -
c
pi
resta
r
t
s
handle files
commit
|
commitdiff
|
tree
2019-05-03
Paul Bauer
Add o
u
tputadapte
r
s (2
/
3)
commit
|
commitdiff
|
tree
2019-05-02
Paul
Bau
e
r
Ad
d
outpu
t
adapters (1/
3
)
commit
|
commitdiff
|
tree
2019-05-02
M
.
Eric I
r
rgang
Infrastructure updat
e
s for depe
n
dent chan
g
es
.
commit
|
commitdiff
|
tree
2019-05-02
Paul Bauer
A
dd
b
u
i
ld
e
r for
T
raje
c
tor
y
FileWriter
commit
|
commitdiff
|
tree
2019-05-02
Ber
k
Hess
Change nbnx
m
F
E
P
p
ointer to uniq
u
e_
p
tr
commit
|
commitdiff
|
tree
2019-05-02
M
ar
k
Abraham
Enhance path search funct
i
o
n
s
commit
|
commitdiff
|
tree
2019-04-30
Mark Abra
h
a
m
Test
t
he ou
t
put
of "gmx mdrun help"
commit
|
commitdiff
|
tree
2019-04-27
Christ
i
an Blau
mrc density map reading
/
writing
commit
|
commitdiff
|
tree
2019-04-27
Chris
t
ian Blau
Three dimen
s
ional coordiante
transfo
r
mation
.
commit
|
commitdiff
|
tree
2019-04-26
Paul Ba
u
er
Add
C
++ coordinate file writin
g
method
.
commit
|
commitdiff
|
tree
2019-04-25
Christian Bl
a
u
density fitting
force
s
commit
|
commitdiff
|
tree
2019-04-25
Paul Bauer
Ad
d
Interf
a
ce to
c
hange coordinate file
i
nfo
commit
|
commitdiff
|
tree
2019-04-25
Mark Abraha
m
Up
d
at
e
style g
u
ide about c
l
as
s
enum
s
commit
|
commitdiff
|
tree
2019-04-23
Ma
r
k Abraham
Clarify pus
h
ing of interaction types
commit
|
commitdiff
|
tree
2019-04-18
Ber
k
H
ess
Remo
v
e nb
n
xm kernel type
f
ro
m
pairlist
generation
commit
|
commitdiff
|
tree
2019-04-18
Berk Hess
Remove c
h
arge groups f
r
o
m do
m
dec and localtop
commit
|
commitdiff
|
tree
2019-04-18
Mark Abraham
Create gmx::compat::
o
p
t
ional
commit
|
commitdiff
|
tree
2019-04-17
Paul Bauer
Ena
b
l
e
p
r
i
n
ting of
k
n
own iss
u
es in comma
n
dline
commit
|
commitdiff
|
tree
2019-04-17
Ma
r
k Abraham
Fix
p
ost-submit
commit
|
commitdiff
|
tree
2019-04-17
Berk Hess
Re
d
uce n
b
nxm CP
U
kernel ar
g
uments
commit
|
commitdiff
|
tree
2019-04-17
Berk Hess
Sim
p
lify nbnxm s
h
ift force handling
commit
|
commitdiff
|
tree
2019-04-16
Szilárd Páll
Move function
s
operating on en
e
rdata ou
t
of
force
.
cpp
commit
|
commitdiff
|
tree
2019-04-16
Berk Hess
S
i
m
p
l
i
f
y
nbnxm
b
uffer clearing
commit
|
commitdiff
|
tree
2019-04-16
B
erk H
e
ss
Rem
o
v
e
RF_excl_correction()
commit
|
commitdiff
|
tree
2019-04-16
Szi
l
árd Páll
Remove "coarse load
balan
c
ing va
r
s" from forc
e
rec
commit
|
commitdiff
|
tree
2019-04-16
Paul Bauer
Refact
o
r
t
_pindex
commit
|
commitdiff
|
tree
2019-04-16
Mark Abraha
m
Removed
mdrun
-gco
m
commit
|
commitdiff
|
tree
2019-04-16
Artem Zhm
u
rov
Fix
for th
e
memory
acc
e
s
s
error in constraints test
.
commit
|
commitdiff
|
tree
2019-04-16
Paul Bauer
Version 2019
.
2
commit
|
commitdiff
|
tree
2019-04-15
Berk
H
ess
Fix pdb-related issues
commit
|
commitdiff
|
tree
2019-04-13
M
ar
k
A
b
ra
h
am
Fix self-c
o
nsisten
c
y
test
s
of hwloc data
st
r
uctur
e
s
commit
|
commitdiff
|
tree
2019-04-12
Mark Abraham
Improve warning messages abou
t
duplicate
d
efinitions
commit
|
commitdiff
|
tree
2019-04-10
Mark
Abraham
Start making IMD
a
n
d s
w
ap m
o
del IMDModul
e
commit
|
commitdiff
|
tree
2019-04-10
Mark A
b
raham
Reuse rvecs_differ in I
n
teract
i
ve
M
D module
commit
|
commitdiff
|
tree
2019-04-10
Mark Abraham
M
a
ke
I
mdS
e
ssion i
n
t
o a Pimpl-ed class wit
h
factory
.
.
.
commit
|
commitdiff
|
tree
2019-04-10
Mark Abraha
m
R
e
form IMD
module
commit
|
commitdiff
|
tree
2019-04-09
M
.
Eric Irrgang
gmxapi 2019 Q1/Q2 project r
o
admap
.
commit
|
commitdiff
|
tree
2019-04-07
Paul Bauer
Remove t_top
o
lo
g
y from t
w
o prepro
c
e
s
s tools
commit
|
commitdiff
|
tree
2019-04-05
Christian Blau
densityfitting -
M
DModu
l
e declaratio
n
commit
|
commitdiff
|
tree
2019-04-05
Davi
d
van
der Spoel
Fixed manual for dihedral rest
r
a
in
t
s
.
commit
|
commitdiff
|
tree
2019-04-05
Szilárd
Páll
Rev
e
rt "
T
emporarily disable ARM HPC compil
e
r in
p
ost
.
.
.
commit
|
commitdiff
|
tree
2019-04-05
S
z
ilárd P
á
ll
Revert "Temp
o
ra
r
ily di
s
able
ARM HPC co
m
piler in post
.
.
.
commit
|
commitdiff
|
tree
2019-04-04
Paul Bauer
U
p
da
t
e
developer guide
f
o
r ch
a
nges to
G
errit
commit
|
commitdiff
|
tree
2019-04-03
M
a
rk Abraham
Initial deactivati
o
n of group sc
h
eme
.
commit
|
commitdiff
|
tree
2019-04-02
Paul Bauer
Refacto
r
gpp_
b
ond_a
t
omtype
commit
|
commitdiff
|
tree
2019-04-02
Paul Bauer
Add s
t
d::string case insensitive compare
commit
|
commitdiff
|
tree
2019-04-02
Paul Bau
e
r
R
e
factor gmx_
g
r
o
u
p
_t
to Sim
u
l
ationAtomGroups
commit
|
commitdiff
|
tree
next