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Merge branch 'origin/release-2020' into merge-2020-into-2021
2020-11-10
Pas
c
a
l
M
erz
Fix MTTK c
o
nstant e
n
ergy bugs
commit
|
commitdiff
|
tree
2020-10-05
Pasc
a
l
Mer
z
Fix Force
B
uff
e
rs
c
o
mpiler warning
commit
|
commitdiff
|
tree
2020-10-01
P
ascal Merz
Update
modular si
m
ula
t
or do
c
s
commit
|
commitdiff
|
tree
2020-09-30
Pa
s
cal Merz
Regression-test-style Google tests for FEP
commit
|
commitdiff
|
tree
2020-09-30
Pascal
M
erz
Fix bug rese
t
t
ing mdatoms
m
asses to
l
a
m
bda=0
state
commit
|
commitdiff
|
tree
2020-09-30
Pascal Merz
Fix #3655
commit
|
commitdiff
|
tree
2020-09-30
Pascal Merz
Fix
#
3694
commit
|
commitdiff
|
tree
2020-09-29
Pasca
l
M
e
rz
Fix bug rese
t
ting mdatoms ma
s
ses to lambda=0 stat
e
commit
|
commitdiff
|
tree
2020-09-27
Pascal Merz
Com
p
are
t
raje
c
tor
i
es to reference data
commit
|
commitdiff
|
tree
2020-09-27
Pascal Merz
Roll back "Ensure the modular simul
a
tor r
u
ns only when
.
.
.
commit
|
commitdiff
|
tree
2020-09-25
Pa
s
c
a
l Merz
Replace
F
r
amesToCompare
enum by
MaxNumFrames
commit
|
commitdiff
|
tree
2020-09-23
Pasc
a
l
M
e
rz
Access write checkpoint
f
u
nctionality directly
commit
|
commitdiff
|
tree
2020-09-23
Pasc
a
l
M
erz
Implem
e
n
t
Berendsen thermost
a
t for modul
a
r simulator
commit
|
commitdiff
|
tree
2020-09-21
Pascal Merz
C
h
e
ckpointda
t
a
D
D
f
ollowup
commit
|
commitdiff
|
tree
2020-09-18
P
a
scal
Mer
z
Refactor v-rescale thermostat
t
o
allow for other algor
i
thms
commit
|
commitdiff
|
tree
2020-09-17
Pascal Mer
z
Rename VRes
c
aleTh
e
rmost
a
t to VelocityScalingTempera
t
ureCoup
l
ing
commit
|
commitdiff
|
tree
2020-09-16
Pas
c
al Merz
I
m
plement mod
u
l
a
r ch
e
c
kpointing
commit
|
commitdiff
|
tree
2020-09-08
P
ascal Merz
Mak
e
legacy energy eleme
n
ts use Checkpoint
D
ata
commit
|
commitdiff
|
tree
2020-09-08
P
a
s
c
a
l M
e
rz
Remove
d
ependency of Energy
D
at
a
o
n
t_state
commit
|
commitdiff
|
tree
2020-09-07
P
a
s
cal
Merz
Make
E
nergyOutput::a
d
dDataAtEnergyStep in
d
ependent
.
.
.
commit
|
commitdiff
|
tree
2020-09-06
Pascal M
e
rz
Pre
p
are legacy checkp
o
int
for modu
l
ar s
i
mulator
checkpointing
commit
|
commitdiff
|
tree
2020-09-06
Pascal Merz
Modular simulator: Simpl
i
f
y
v
e
locity u
p
date dispat
c
h
commit
|
commitdiff
|
tree
2020-09-04
Pasca
l
Merz
Introd
u
ce CheckpointDat
a
commit
|
commitdiff
|
tree
2020-09-03
Pa
s
cal
M
erz
R
e
move unn
e
ce
s
sary
friend de
c
l
a
ration
commit
|
commitdiff
|
tree
2020-09-03
P
asc
a
l Merz
Make dd_collect_
v
e
c
independent of t_
s
tate
commit
|
commitdiff
|
tree
2020-08-17
Pa
s
cal
Merz
Use
p
roper doxy
g
en tags in modular simulator
commit
|
commitdiff
|
tree
2020-08-16
Pa
s
cal
M
erz
Mod
u
la
r
simulator:
Don't wrap std
:
:funct
i
o
n
in unique_ptr
commit
|
commitdiff
|
tree
2020-08-14
Pascal Merz
I
n
t
r
o
du
c
e flexible Mod
u
larSimulatorA
l
go
r
ithmBuilder
.
.
.
commit
|
commitdiff
|
tree
2020-08-07
Pascal Merz
Introduce Glo
b
a
l
C
o
mmunicationHe
l
per
commit
|
commitdiff
|
tree
2020-08-07
Pa
s
cal Mer
z
Improve
modular
s
i
m
u
lator buil
d
er
s
commit
|
commitdiff
|
tree
2020-08-07
Pascal Merz
S
eparate
ISimulator interfac
e
and data
commit
|
commitdiff
|
tree
2020-07-18
Pa
s
cal Merz
Follow up to
"Separate
S
tateP
r
opagatorData e
l
ement
.
.
.
commit
|
commitdiff
|
tree
2020-07-17
Pa
s
cal Mer
z
Introduce
modular simu
l
a
tor
exceptions
commit
|
commitdiff
|
tree
2020-07-15
Pasc
a
l
Merz
Separate Element from F
r
e
e
Ener
g
yPer
t
urb
a
t
i
onD
a
t
a
commit
|
commitdiff
|
tree
2020-07-14
Pasc
a
l Merz
S
eparate energy d
a
ta and element
commit
|
commitdiff
|
tree
2020-07-09
P
a
scal Merz
D
i
v
ide
d
efault communicator from DD communicators
commit
|
commitdiff
|
tree
2020-07-08
Pascal Merz
S
e
p
arate State
P
ropagatorData
e
lemen
t
commit
|
commitdiff
|
tree
2020-07-07
Pa
s
cal Merz
A
nnotate modul
a
r simul
a
tor headers
w
ith exposur
e
le
v
el
commit
|
commitdiff
|
tree
2020-07-03
Pascal
Merz
Separate Modula
r
S
imulator and ModularSimulator
A
lg
o
rithm
commit
|
commitdiff
|
tree
2020-06-23
Pascal
Merz
Refactor simulator compariso
n
tests
commit
|
commitdiff
|
tree
2020-06-18
Pascal Merz
Mod
u
lar simulator: Separat
e
trajectory
e
l
ement
a
nd
.
.
.
commit
|
commitdiff
|
tree
2020-06-17
Pasc
a
l
Merz
Fi
x
s
ty
l
e error
s
in
m
odul
a
r s
i
mulator
propag
a
tor
commit
|
commitdiff
|
tree
2020-05-04
Pascal Merz
Catch erro
r
s in
v
-rescale and Parrine
l
lo-Rahman ch
e
ckp
o
inting
commit
|
commitdiff
|
tree
2020-04-23
Pascal
M
erz
Mak
e
boxdeformation indep
e
nden
t
o
f t_comm
r
ec
commit
|
commitdiff
|
tree
2020-04-22
Pascal Merz
Make
i
nit
_
dir
e
s indepe
n
dent of t_commrec
commit
|
commitdiff
|
tree
2020-04-17
P
asc
a
l Mer
z
M
a
ke global topolo
g
y const in ISimulator
commit
|
commitdiff
|
tree
2020-04-14
Pascal
M
e
rz
Make bonded int
e
ra
c
tion c
h
ecking more robust
(
modular
.
.
.
commit
|
commitdiff
|
tree
2020-04-14
Pas
c
al Merz
Reintroduce LJ Ewald tables
commit
|
commitdiff
|
tree
2020-04-07
Pascal Merz
Merge f
o
rce and s
h
ellF
C
elements
commit
|
commitdiff
|
tree
2020-04-07
Pascal Me
r
z
Require explicit MP
I
_COMM for gmx_bcast and gmx_barrier
commit
|
commitdiff
|
tree
2020-04-07
Pascal Merz
Make globa
l
topology constant in energyO
u
tput
.
printAnneal
i
ng
.
.
.
commit
|
commitdiff
|
tree
2020-04-07
Pascal M
e
r
z
Make global topology const in m
i
ni
m
i
z
ation
commit
|
commitdiff
|
tree
2020-04-06
Pa
s
cal Merz
Make
global
t
opology con
s
tant in mdoutf
commit
|
commitdiff
|
tree
2020-04-06
Pascal Merz
Make bonded
inte
r
actio
n
checking more robu
s
t (
m
odul
a
r
.
.
.
commit
|
commitdiff
|
tree
2020-04-03
Pascal Me
r
z
Fix e
x
p
a
nded ensemble on c
h
eckp
o
int resta
r
ts
commit
|
commitdiff
|
tree
2020-02-27
P
asca
l
M
e
rz
Loose
n
gmxapi stops
i
gn
a
ler test
commit
|
commitdiff
|
tree
2020-02-27
Pascal Merz
U
s
e legacy c
o
d
e
path for t_graph (mo
d
u
l
ar simulat
o
r)
commit
|
commitdiff
|
tree
2020-02-27
Pascal Merz
E
x
tract and exp
o
se fu
n
ction to determine whether mole
c
ules
.
.
.
commit
|
commitdiff
|
tree
2020-02-26
Pascal Mer
z
Fix c
o
ns
t
raint contribut
i
on to dhdl (mo
d
ul
a
r sim
u
lator)
commit
|
commitdiff
|
tree
2020-02-26
Pascal Merz
Fix calculation of reciprocal terms in reru
n
commit
|
commitdiff
|
tree
2020-02-24
Pas
c
al Merz
Use Arra
y
Re
f
in
c
ompute_glo
b
als
commit
|
commitdiff
|
tree
2020-02-21
Pascal Merz
Us
e
l
e
gacy
code pa
t
h
for NMR re
s
tra
i
nts (modular simulat
o
r
)
commit
|
commitdiff
|
tree
2020-02-21
Pa
s
cal Me
r
z
C
o
r
rect for skewe
d
box i
n
non-DD
m
odular simulator
commit
|
commitdiff
|
tree
2020-02-14
Pasca
l
Merz
Expand test coverage o
f
exa
c
t continuation tests
commit
|
commitdiff
|
tree
2020-02-14
Pascal Merz
Fix reading o
f
checkpoi
n
ts wit
h
Parrinello-
R
ah
m
a
n
.
.
.
commit
|
commitdiff
|
tree
2020-02-14
Pascal Merz
Fix Parrinel
l
o
-
R
ahma
n
scaling on i
n
i
tial
s
tep (modular
.
.
.
commit
|
commitdiff
|
tree
2020-02-14
Pasc
a
l Merz
Move modular si
m
u
lator
d
e
c
i
s
i
o
n before checkpoint loadin
g
commit
|
commitdiff
|
tree
2020-02-13
Pascal Merz
Fix
c
heckNumberOfBondedIntera
c
tions
b
ug
commit
|
commitdiff
|
tree
2020-02-13
Pas
c
al Merz
Exp
o
se vsite
c
oun
t
i
n
g
commit
|
commitdiff
|
tree
2020-02-05
Pascal Merz
Test
P
add
e
dV
e
ctor to ArrayRef conve
r
s
ion
commit
|
commitdiff
|
tree
2020-02-05
Pascal Merz
M
i
n
or impr
o
vem
e
nt
s
to v
c
m
.
cpp
commit
|
commitdiff
|
tree
2020-02-05
Pas
c
al
Merz
Merge VV i
m
pleme
n
tations of
ComputeGl
o
balsElement
commit
|
commitdiff
|
tree
2020-01-31
Pa
s
cal M
e
r
z
Mod
u
la
r
simulator:
A
llow f
o
r n
u
l
lptr
i
n
e
lement list
.
.
.
commit
|
commitdiff
|
tree
2020-01-31
Pascal Merz
StatePr
o
pagatorData: Make c
o
nst box gett
e
rs const
functions
commit
|
commitdiff
|
tree
2020-01-31
Pascal Merz
Make t
_
inputrec const in C
o
mputeGlobalsElem
e
nt
commit
|
commitdiff
|
tree
2019-12-17
Pas
c
al Me
r
z
Fix exact
c
ontinuat
i
on modula
r
simula
t
or
commit
|
commitdiff
|
tree
2019-12-12
Pascal Merz
Tes
t
f
or
expected output fil
e
s
commit
|
commitdiff
|
tree
2019-12-12
Pascal Merz
F
ix f
i
nal configuratio
n
writing for mod
u
lar simulator
commit
|
commitdiff
|
tree
2019-10-31
Pascal
M
er
z
Che
c
k
for contradicting environment var
i
ables
(
modular
.
.
.
commit
|
commitdiff
|
tree
2019-10-30
Pascal Merz
Fix dox
y
gen for mo
d
u
lar simu
l
ator
commit
|
commitdiff
|
tree
2019-10-30
Pascal Merz
F
i
x mo
d
u
lar si
m
ulator documentat
i
on
commit
|
commitdiff
|
tree
2019-10-29
P
a
s
cal Merz
F
i
x compati
b
ility c
h
eck of
modular simu
l
a
tor
commit
|
commitdiff
|
tree
2019-10-27
Pascal Merz
E
nable forced rotation for
m
odular simul
a
tor
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
Co
r
re
c
t fo
r
ske
w
ed box b
e
fore dom
a
in de
c
ompos
i
t
i
on
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
Fi
x
log w
r
iting (mo
d
ular
s
imu
l
ator
)
commit
|
commitdiff
|
tree
2019-10-23
Pascal
Merz
Ada
p
t enum to s
t
yle conventi
o
n (mod
u
la
r
s
imulator)
commit
|
commitdiff
|
tree
2019-10-23
P
ascal Mer
z
Smal
l
improve
m
en
t
to
E
nergyElement
(
modular simula
t
o
r
)
commit
|
commitdiff
|
tree
2019-10-22
Pascal Merz
Fi
x
st
o
p co
n
dit
i
o
n
handl
i
ng
(
modu
l
ar s
i
mulat
o
r
)
commit
|
commitdiff
|
tree
2019-10-22
Pascal Merz
Fix signal propaga
t
ion (modular
s
imula
t
or)
commit
|
commitdiff
|
tree
2019-10-22
Pas
c
al Merz
Fix
D
omDe
c
step (modu
l
a
r simulato
r
)
commit
|
commitdiff
|
tree
2019-10-22
Pascal
M
e
rz
Fix PmeLoadBalance
H
elper
i
nit
i
ali
z
ation (modular
simu
l
ator)
commit
|
commitdiff
|
tree
2019-10-01
Pasc
a
l Merz
Output c
o
rrect kinetic at last
s
te
p
(modular
simulator
)
commit
|
commitdiff
|
tree
2019-09-23
Pas
c
al
M
erz
Parrinello
-
Rahm
a
n f
o
r md-v
v
commit
|
commitdiff
|
tree
2019-09-23
Pascal
Merz
Pa
r
rinello-Rahman ba
r
ostat for mod
u
l
a
r s
i
mula
t
or (leap
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
Z
er
o
pressure
and virial te
n
sors at begi
n
n
in
g
of step
commit
|
commitdiff
|
tree
2019-09-23
Pascal Me
r
z
Intr
o
du
c
e
FEP into modular s
i
mulator
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
Ma
k
e
Che
c
kpoint
H
elper
safer and ea
s
ier to use
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
Fix vrescale th
e
rmostat in
t
egral (modular simulator)
commit
|
commitdiff
|
tree
2019-09-20
Pascal Merz
Fix restarts in modular simulator
commit
|
commitdiff
|
tree
2019-09-20
P
a
scal Merz
Fi
x
domdec for md-
v
v modula
r
s
imulator
commit
|
commitdiff
|
tree
next