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GROMACS 2021 first beta release
2020-10-05
P
asca
l
Merz
Fix ForceBuf
f
ers compiler warn
i
ng
commit
|
commitdiff
|
tree
2020-10-01
Pascal Merz
Update m
o
dul
a
r
simu
l
a
t
or docs
commit
|
commitdiff
|
tree
2020-09-30
Pascal Mer
z
Regressio
n
-te
s
t
-
s
tyle Goo
g
le tests fo
r
FEP
commit
|
commitdiff
|
tree
2020-09-30
Pascal Merz
Fix b
u
g r
e
sett
i
ng mdatoms masses to lambda=0 state
commit
|
commitdiff
|
tree
2020-09-30
Pascal Me
r
z
Fix #3655
commit
|
commitdiff
|
tree
2020-09-30
P
ascal Merz
Fi
x
#3694
commit
|
commitdiff
|
tree
2020-09-29
Pascal Me
r
z
F
i
x bug resettin
g
m
da
t
oms
m
a
s
s
e
s to lambd
a
=
0 state
commit
|
commitdiff
|
tree
2020-09-27
Pa
s
cal M
e
rz
Compare t
r
a
j
e
ctories to refer
e
nce da
t
a
commit
|
commitdiff
|
tree
2020-09-27
Pascal Merz
Roll back "Ensure the
m
odular simul
a
tor runs
only wh
e
n
.
.
.
commit
|
commitdiff
|
tree
2020-09-25
Pascal Merz
Re
p
lace Fra
m
esToCompare enum by MaxNumFrames
commit
|
commitdiff
|
tree
2020-09-23
Pa
s
cal Merz
Ac
c
ess write
checkpoi
n
t funct
i
o
n
a
l
ity di
r
ectly
commit
|
commitdiff
|
tree
2020-09-23
Pascal Merz
Implemen
t
Berendsen thermostat
f
or
m
o
dular si
m
ul
a
tor
commit
|
commitdiff
|
tree
2020-09-21
Pasc
a
l Merz
Checkpointdata D
D
followup
commit
|
commitdiff
|
tree
2020-09-18
Pascal Merz
Refac
t
or v-rescale the
r
mostat to allow for
o
ther algori
t
hms
commit
|
commitdiff
|
tree
2020-09-17
Pascal Merz
Rename VRescaleT
h
e
rm
o
sta
t
to Velo
c
ityScalingTemp
e
r
atureCoupling
commit
|
commitdiff
|
tree
2020-09-16
Pascal Merz
Implemen
t
mo
d
ular checkpoi
n
ting
commit
|
commitdiff
|
tree
2020-09-08
Pascal Merz
Make legacy
energy elements use CheckpointData
commit
|
commitdiff
|
tree
2020-09-08
Pa
s
cal
M
erz
Re
m
ove dep
e
nden
c
y o
f
E
nergyData on t_s
t
ate
commit
|
commitdiff
|
tree
2020-09-07
Pasca
l
Merz
Ma
k
e EnergyOutp
u
t
:
:
addDat
a
AtEnerg
y
Step independent
.
.
.
commit
|
commitdiff
|
tree
2020-09-06
Pascal
Merz
Prepa
r
e lega
c
y check
p
o
i
n
t for modular si
m
ulato
r
checkp
o
int
i
ng
commit
|
commitdiff
|
tree
2020-09-06
Pascal
Merz
Modul
a
r simulator:
Simplify
velocity update di
s
patch
commit
|
commitdiff
|
tree
2020-09-04
Pascal Merz
Introduce
C
heckpointData
commit
|
commitdiff
|
tree
2020-09-03
Pascal Merz
Remove unneces
s
ary friend decl
a
r
a
tion
commit
|
commitdiff
|
tree
2020-09-03
Pasc
a
l Merz
Mak
e
d
d
_
collect_
v
ec independen
t
of t_
s
tate
commit
|
commitdiff
|
tree
2020-08-17
Pascal
M
erz
Use p
r
oper dox
y
ge
n
tags in modular simula
t
or
commit
|
commitdiff
|
tree
2020-08-16
P
ascal Merz
Modula
r
simu
l
ator:
Don't
w
rap std::
f
uncti
o
n
in unique_ptr
commit
|
commitdiff
|
tree
2020-08-14
P
a
scal
M
erz
Introduce f
l
e
x
i
ble Modu
l
arSim
u
latorAlgorith
m
Builder
.
.
.
commit
|
commitdiff
|
tree
2020-08-07
Pascal
M
erz
In
t
roduce Globa
l
CommunicationHelper
commit
|
commitdiff
|
tree
2020-08-07
Pascal Merz
Improve modular simulator builde
r
s
commit
|
commitdiff
|
tree
2020-08-07
P
ascal Merz
Sep
a
rate ISimulator
i
nt
e
rface and dat
a
commit
|
commitdiff
|
tree
2020-07-18
Pascal Me
r
z
Follow up to "
S
eparate S
t
a
tePropa
g
atorData eleme
n
t
.
.
.
commit
|
commitdiff
|
tree
2020-07-17
Pascal
Merz
I
ntroduce modular simul
a
tor exceptions
commit
|
commitdiff
|
tree
2020-07-15
Pascal Merz
Separa
t
e Element from F
r
eeEnergyPe
r
turba
t
ionData
commit
|
commitdiff
|
tree
2020-07-14
Pascal Merz
Se
p
arate energy data
an
d
el
e
ment
commit
|
commitdiff
|
tree
2020-07-09
Pas
c
al Merz
Di
v
i
de default communicat
o
r from DD co
m
m
u
nica
t
o
r
s
commit
|
commitdiff
|
tree
2020-07-08
P
ascal Merz
Separate StatePropagatorData
e
lement
commit
|
commitdiff
|
tree
2020-07-07
Pascal Merz
Annotate m
o
dular simulator
headers
wit
h
expos
u
re level
commit
|
commitdiff
|
tree
2020-07-03
P
a
scal Merz
Separa
t
e ModularSimula
t
or and Mo
d
ularSimulatorAlgorit
h
m
commit
|
commitdiff
|
tree
2020-06-23
Pascal Me
r
z
Refactor simulato
r
comparison tests
commit
|
commitdiff
|
tree
2020-06-18
Pascal Merz
Modula
r
simulator: Sep
a
rate
tra
j
ectory element and
.
.
.
commit
|
commitdiff
|
tree
2020-06-17
Pascal Merz
Fix style errors in
modular simulato
r
propagator
commit
|
commitdiff
|
tree
2020-05-04
Pascal Merz
Catch errors i
n
v-resca
l
e and Parrinello-Rahman chec
k
pointing
commit
|
commitdiff
|
tree
2020-04-23
Pasc
a
l M
e
rz
Mak
e
boxde
f
ormation indepe
n
dent of t_comm
r
e
c
commit
|
commitdiff
|
tree
2020-04-22
Pasc
a
l Merz
Mak
e
init
_
d
ires
i
ndepe
n
de
n
t
of t_commrec
commit
|
commitdiff
|
tree
2020-04-17
Pa
s
cal M
e
rz
M
a
ke glob
a
l t
o
pology const i
n
I
S
imulat
o
r
commit
|
commitdiff
|
tree
2020-04-14
Pascal Mer
z
Make bonded interaction checking m
o
re robust (modular
.
.
.
commit
|
commitdiff
|
tree
2020-04-14
Pascal Merz
Reintrod
u
ce LJ Ewal
d
tables
commit
|
commitdiff
|
tree
2020-04-07
Pa
s
cal Merz
Merge force and shel
l
FC eleme
n
t
s
commit
|
commitdiff
|
tree
2020-04-07
Pascal M
e
rz
Require expli
c
i
t MPI_COMM fo
r
gmx_bcast
a
n
d gmx_b
a
rrier
commit
|
commitdiff
|
tree
2020-04-07
Pascal M
e
rz
M
ake
g
loba
l
topology cons
t
ant i
n
energyOutput
.
printAn
n
ealin
g
.
.
.
commit
|
commitdiff
|
tree
2020-04-07
P
a
s
cal Merz
Make g
l
oba
l
topology const in minimization
commit
|
commitdiff
|
tree
2020-04-06
Pasc
a
l Merz
M
a
ke global to
p
ology
consta
n
t in mdoutf
commit
|
commitdiff
|
tree
2020-04-06
Pasca
l
Merz
Make bo
n
d
e
d
i
n
t
er
a
ction checking mor
e
robust
(
m
o
dular
.
.
.
commit
|
commitdiff
|
tree
2020-04-03
Pascal
Merz
F
i
x expanded ensemble on
c
heckpoint restar
t
s
commit
|
commitdiff
|
tree
2020-02-27
P
a
scal
Merz
Lo
o
sen gmxapi stopsignaler test
commit
|
commitdiff
|
tree
2020-02-27
Pascal
M
erz
Use legacy
cod
e
p
a
th for t_graph (modular s
i
mulator)
commit
|
commitdiff
|
tree
2020-02-27
Pascal
Mer
z
Ex
t
r
a
ct and expose functi
o
n to d
e
termine
whet
h
e
r mole
c
ule
s
.
.
.
commit
|
commitdiff
|
tree
2020-02-26
Pascal Merz
Fix c
o
nstraint contri
b
ution
t
o dh
d
l (m
o
dular
s
imulator
)
commit
|
commitdiff
|
tree
2020-02-26
Pascal
Merz
F
ix calcula
t
ion o
f
re
c
iprocal terms in re
r
u
n
commit
|
commitdiff
|
tree
2020-02-24
P
a
scal Merz
Use ArrayRef in comp
u
te_gl
o
ba
l
s
commit
|
commitdiff
|
tree
2020-02-21
P
ascal
M
erz
Use le
g
a
cy
c
ode
path for NMR restraints (
m
odu
l
ar simulat
o
r)
commit
|
commitdiff
|
tree
2020-02-21
Pascal M
e
rz
C
o
rrect
f
o
r skewed box in
n
on
-
DD m
o
dular simula
t
or
commit
|
commitdiff
|
tree
2020-02-14
Pascal Merz
E
x
pan
d
tes
t
c
o
v
erage of e
x
a
c
t
cont
i
nuati
o
n tests
commit
|
commitdiff
|
tree
2020-02-14
Pascal Merz
F
i
x reading of
c
he
c
k
points
wit
h
Parrinello-Rahman
.
.
.
commit
|
commitdiff
|
tree
2020-02-14
Pascal Merz
Fix Parrinello-R
a
h
m
an scal
i
ng on initial step (modular
.
.
.
commit
|
commitdiff
|
tree
2020-02-14
Pascal Merz
Move mod
u
lar simulator decision before
c
hec
k
po
i
n
t
loading
commit
|
commitdiff
|
tree
2020-02-13
Pascal Mer
z
Fix che
c
kNumbe
r
OfBondedInterac
t
ions bug
commit
|
commitdiff
|
tree
2020-02-13
P
ascal
M
erz
Expose
vs
i
te coun
t
ing
commit
|
commitdiff
|
tree
2020-02-05
Pasc
a
l Merz
Test Pa
d
d
e
dVe
c
tor to ArrayRef
conversi
o
n
commit
|
commitdiff
|
tree
2020-02-05
P
as
c
al M
e
r
z
Minor
i
mpro
v
ement
s
t
o
vcm
.
cpp
commit
|
commitdiff
|
tree
2020-02-05
Pascal Merz
Merg
e
VV implementations of ComputeGlo
b
a
ls
E
lement
commit
|
commitdiff
|
tree
2020-01-31
P
a
scal Merz
Mo
d
ul
a
r s
i
m
u
lator: Allow for nullptr in
e
l
ement
list
.
.
.
commit
|
commitdiff
|
tree
2020-01-31
P
ascal Me
r
z
S
t
atePropagatorData: Make const b
o
x gett
e
rs const functions
commit
|
commitdiff
|
tree
2020-01-31
Pascal
M
e
r
z
Ma
k
e t_in
p
ut
r
ec const i
n
ComputeG
l
obalsEle
m
e
n
t
commit
|
commitdiff
|
tree
2019-12-17
P
a
scal
Merz
Fix exact co
n
tinuatio
n
modular simula
t
or
commit
|
commitdiff
|
tree
2019-12-12
Pascal
Merz
Test for expected
o
utput files
commit
|
commitdiff
|
tree
2019-12-12
Pascal Merz
Fix
fin
a
l configu
r
ation writing fo
r
modu
l
ar simulator
commit
|
commitdiff
|
tree
2019-10-31
Pas
c
al M
e
rz
Check for con
t
radictin
g
e
n
vi
r
onment
variables (modul
a
r
.
.
.
commit
|
commitdiff
|
tree
2019-10-30
Pascal M
e
rz
Fi
x
doxyge
n
f
or mo
d
ular
s
imulator
commit
|
commitdiff
|
tree
2019-10-30
P
ascal Merz
Fix mod
u
lar
simulator documentation
commit
|
commitdiff
|
tree
2019-10-29
P
ascal Merz
Fix compatibility ch
e
ck of
modular
simulator
commit
|
commitdiff
|
tree
2019-10-27
P
a
scal Mer
z
Enable forced r
o
tati
o
n for
modular simulator
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
C
o
rrec
t
for
s
k
ewed box
b
e
fore domain
d
ecom
p
o
sition
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
P
a
sc
a
l
M
e
rz
Fix
log
writing (modula
r
simulat
o
r)
commit
|
commitdiff
|
tree
2019-10-23
Pas
c
al
M
e
rz
Ad
a
pt enu
m
to style convention (m
o
d
u
lar simulator
)
commit
|
commitdiff
|
tree
2019-10-23
Pascal Me
r
z
Sma
l
l
improvement to EnergyElement (
m
od
u
lar simulator
)
commit
|
commitdiff
|
tree
2019-10-22
P
ascal Merz
Fix stop condi
t
ion ha
n
dl
i
ng (mo
d
ula
r
simulator
)
commit
|
commitdiff
|
tree
2019-10-22
P
a
s
c
al M
e
rz
Fix
si
g
nal
p
r
o
pa
g
ation (modular simul
a
tor)
commit
|
commitdiff
|
tree
2019-10-22
Pascal Me
r
z
Fix
D
om
D
ec step
(modular simulator)
commit
|
commitdiff
|
tree
2019-10-22
Pascal
M
e
r
z
Fix
PmeLoa
d
BalanceH
e
lper initialization (modular simulator)
commit
|
commitdiff
|
tree
2019-10-01
Pascal Merz
Out
p
ut correct kinetic at las
t
s
tep (modular simulator)
commit
|
commitdiff
|
tree
2019-09-23
Pasc
a
l
Me
r
z
Parrinello-Rahman for md-vv
commit
|
commitdiff
|
tree
2019-09-23
P
a
scal Merz
Parrine
l
lo-Rahman
barostat for
m
odular simulator (lea
p
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
Pasca
l
Merz
Zero pres
s
u
re
and virial tensors at be
g
inning of
step
commit
|
commitdiff
|
tree
2019-09-23
Pa
s
cal
M
erz
Int
r
od
u
ce
F
E
P into modu
l
ar simulator
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
Make Chec
k
pointHelper
s
afer and easier to u
s
e
commit
|
commitdiff
|
tree
2019-09-23
Pascal Me
r
z
Fix vrescale thermost
a
t integra
l
(modular simulator)
commit
|
commitdiff
|
tree
2019-09-20
Pascal M
e
rz
Fix re
s
tar
t
s
in modu
l
ar simulat
o
r
commit
|
commitdiff
|
tree
2019-09-20
Pascal Merz
Fix domdec for md-v
v
m
o
d
u
l
a
r simulator
commit
|
commitdiff
|
tree
2019-09-20
P
a
s
cal
Merz
Run simulator equiv
a
lence te
s
ts
i
n double pr
e
cision
.
.
.
commit
|
commitdiff
|
tree
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