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Update instructions in containers.rst
2020-11-10
Pa
s
cal Merz
Fix
MTTK constant ener
g
y bugs
commit
|
commitdiff
|
tree
2020-10-05
Pascal Merz
Fix Force
B
uff
e
rs compiler
w
arning
commit
|
commitdiff
|
tree
2020-10-01
Pascal
Me
r
z
Upda
t
e modular simulator docs
commit
|
commitdiff
|
tree
2020-09-30
Pascal
M
e
rz
Regressio
n
-test-style Goo
g
le tes
t
s for
F
EP
commit
|
commitdiff
|
tree
2020-09-30
Pa
s
cal Merz
F
i
x bug res
e
t
ti
n
g m
d
atoms masse
s
to lambda=0 state
commit
|
commitdiff
|
tree
2020-09-30
Pascal Merz
Fix #3655
commit
|
commitdiff
|
tree
2020-09-30
Pas
c
al Merz
Fix
#
3694
commit
|
commitdiff
|
tree
2020-09-29
Pascal Merz
Fix bug rese
t
ting mdat
o
m
s
masses to lambda=
0
state
commit
|
commitdiff
|
tree
2020-09-27
Pascal Mer
z
Compare t
r
ajectories to r
e
ferenc
e
da
t
a
commit
|
commitdiff
|
tree
2020-09-27
P
a
scal
M
erz
R
oll back
"E
n
sur
e
the
modular simulator runs only when
.
.
.
commit
|
commitdiff
|
tree
2020-09-25
Pascal Merz
R
e
pla
c
e F
r
amesToCompare enum b
y
MaxNumFrames
commit
|
commitdiff
|
tree
2020-09-23
P
asc
a
l Me
r
z
Acc
e
ss wr
i
te checkpoint functionality dir
e
ctly
commit
|
commitdiff
|
tree
2020-09-23
Pascal Merz
Implem
e
nt Berendsen thermostat for modu
l
a
r sim
u
lator
commit
|
commitdiff
|
tree
2020-09-21
Pasca
l
Merz
Checkpoint
d
at
a
DD
f
ollowup
commit
|
commitdiff
|
tree
2020-09-18
Pascal
M
erz
Refactor v-r
e
scale thermo
s
tat to al
l
ow for other a
l
gorithms
commit
|
commitdiff
|
tree
2020-09-17
Pa
s
cal Merz
R
e
nam
e
VRescaleThermostat to VelocityScalingTemperatureCo
u
pling
commit
|
commitdiff
|
tree
2020-09-16
Pasca
l
Merz
Impl
e
ment modu
l
ar check
p
ointing
commit
|
commitdiff
|
tree
2020-09-08
Pascal Merz
Make legacy energy elements us
e
C
h
eckpointData
commit
|
commitdiff
|
tree
2020-09-08
Pasc
a
l Merz
Remove
d
ependency of EnergyData
o
n t_state
commit
|
commitdiff
|
tree
2020-09-07
P
asca
l
Merz
Make EnergyOutput
:
:a
d
dDat
a
AtEn
e
r
gyStep ind
e
pendent
.
.
.
commit
|
commitdiff
|
tree
2020-09-06
Pasca
l
Merz
Prepar
e
legacy
c
heckpoint for modu
l
a
r
simulator checkpointing
commit
|
commitdiff
|
tree
2020-09-06
Pascal M
e
rz
Modular simulat
o
r: Simplify
v
eloci
t
y update
d
isp
a
t
ch
commit
|
commitdiff
|
tree
2020-09-04
P
a
scal Merz
I
nt
r
oduce C
h
eckpoint
D
a
t
a
commit
|
commitdiff
|
tree
2020-09-03
Pascal Merz
Remove unnec
e
s
s
ary friend
de
c
laration
commit
|
commitdiff
|
tree
2020-09-03
Pascal
M
erz
Make
dd_colle
c
t_vec indepen
d
e
nt of t_
s
t
a
te
commit
|
commitdiff
|
tree
2020-08-17
P
a
scal
Mer
z
Use pr
o
per doxygen tags in modula
r
sim
u
lat
o
r
commit
|
commitdiff
|
tree
2020-08-16
Pasca
l
Me
r
z
Modular simulator: Don't wrap st
d
:
:
function in un
i
q
u
e_ptr
commit
|
commitdiff
|
tree
2020-08-14
Pas
c
a
l
M
erz
Introduce flexi
b
le
M
odu
l
arSimu
l
atorAlgorit
h
mBuilder
.
.
.
commit
|
commitdiff
|
tree
2020-08-07
P
asc
a
l
M
erz
Intro
d
uce Glo
b
alCommu
n
i
c
at
i
onHelper
commit
|
commitdiff
|
tree
2020-08-07
P
asc
a
l
M
erz
I
m
p
rove m
o
dul
a
r
sim
u
lator b
u
ilders
commit
|
commitdiff
|
tree
2020-08-07
Pascal Merz
Sep
a
rate
I
S
im
u
l
a
t
o
r interface and
d
ata
commit
|
commitdiff
|
tree
2020-07-18
Pascal Me
r
z
Follow up to "Separate St
a
tePropaga
t
orData element
.
.
.
commit
|
commitdiff
|
tree
2020-07-17
Pasc
a
l
M
e
r
z
Introd
u
ce modular sim
u
lator
ex
c
eptions
commit
|
commitdiff
|
tree
2020-07-15
Pasc
a
l M
e
rz
Separate Element f
r
om Fr
e
eEnergyPerturbationData
commit
|
commitdiff
|
tree
2020-07-14
Pascal Merz
Separate energ
y
d
a
ta and ele
m
ent
commit
|
commitdiff
|
tree
2020-07-09
Pascal Merz
Divide
d
efault
c
ommunicator
f
rom DD
c
ommuni
c
ators
commit
|
commitdiff
|
tree
2020-07-08
Pasca
l
M
e
rz
Separate St
a
tePro
p
a
g
atorData el
e
men
t
commit
|
commitdiff
|
tree
2020-07-07
Pascal Merz
Anno
t
a
te m
o
dular sim
u
l
a
tor
headers with expo
s
u
r
e
level
commit
|
commitdiff
|
tree
2020-07-03
Pascal Merz
Sep
a
rat
e
Modular
S
imula
t
or and ModularSimulato
r
Algor
i
thm
commit
|
commitdiff
|
tree
2020-06-23
Pascal Merz
Refactor
s
imul
a
tor comparis
o
n te
s
t
s
commit
|
commitdiff
|
tree
2020-06-18
Pascal Mer
z
Modu
l
ar s
i
mulat
o
r: Se
p
arate
tra
j
ector
y
elem
e
nt and
.
.
.
commit
|
commitdiff
|
tree
2020-06-17
Pascal
M
erz
F
i
x styl
e
e
rrors
in modular simulator
p
ropagator
commit
|
commitdiff
|
tree
2020-05-04
Pascal Me
r
z
Catch errors
i
n
v-re
s
cale and Parrinello-Rahman check
p
oi
n
ting
commit
|
commitdiff
|
tree
2020-04-23
Pa
s
cal Merz
Make bo
x
deformation
i
n
dependent of t_c
o
m
m
rec
commit
|
commitdiff
|
tree
2020-04-22
Pasc
a
l Merz
Make in
i
t_dires independen
t
of t_commre
c
commit
|
commitdiff
|
tree
2020-04-17
P
a
s
c
al Merz
Make
g
lob
a
l
t
o
p
o
log
y
c
o
nst in ISimulator
commit
|
commitdiff
|
tree
2020-04-14
Pascal Merz
Make bonde
d
i
nteraction checki
n
g more robust (mod
u
lar
.
.
.
commit
|
commitdiff
|
tree
2020-04-14
Pascal Me
r
z
Reintr
o
duce LJ
E
w
a
l
d
t
a
ble
s
commit
|
commitdiff
|
tree
2020-04-07
Pasc
a
l Merz
Merge f
o
r
c
e and
s
h
el
l
FC elements
commit
|
commitdiff
|
tree
2020-04-07
Pasc
a
l Merz
Require explici
t
MPI_C
O
M
M
fo
r
gmx_bcast and gmx_bar
r
ier
commit
|
commitdiff
|
tree
2020-04-07
Pascal Merz
M
ake global topology constant in energyOut
p
ut
.
printAnneal
i
ng
.
.
.
commit
|
commitdiff
|
tree
2020-04-07
Pas
c
al Merz
Make globa
l
topo
l
og
y
cons
t
in minimizati
o
n
commit
|
commitdiff
|
tree
2020-04-06
Pascal Merz
M
a
k
e g
l
oba
l
topology
c
onstant in
mdoutf
commit
|
commitdiff
|
tree
2020-04-06
Pascal M
e
rz
Make bonded interaction check
i
n
g more ro
b
ust
(
modular
.
.
.
commit
|
commitdiff
|
tree
2020-04-03
Pascal Merz
Fix expande
d
ensemble on chec
k
point restar
t
s
commit
|
commitdiff
|
tree
2020-02-27
P
asc
a
l Mer
z
Loosen
gm
x
api stopsignaler
t
est
commit
|
commitdiff
|
tree
2020-02-27
P
a
scal Mer
z
Use legacy code path for t_
g
raph (modular si
m
ulator)
commit
|
commitdiff
|
tree
2020-02-27
P
a
scal Merz
Extract and exp
o
se function to de
t
ermine whether molecules
.
.
.
commit
|
commitdiff
|
tree
2020-02-26
Pa
s
cal
Merz
Fix con
s
traint contrib
u
ti
o
n to d
h
dl (
m
odular
s
i
mu
l
a
t
or
)
commit
|
commitdiff
|
tree
2020-02-26
Pascal Mer
z
Fix calculation o
f
reciproc
a
l terms in re
r
u
n
commit
|
commitdiff
|
tree
2020-02-24
Pa
s
cal
M
erz
Us
e
Array
R
e
f
in c
o
mpute_gl
o
b
a
ls
commit
|
commitdiff
|
tree
2020-02-21
Pascal Merz
Use legac
y
c
o
de pa
t
h for NMR restraints (modu
l
a
r
simulator)
commit
|
commitdiff
|
tree
2020-02-21
Pascal Merz
Co
r
rect for s
k
ewed b
o
x i
n
non-DD m
o
dular simulator
commit
|
commitdiff
|
tree
2020-02-14
Pascal Mer
z
Expand test covera
g
e
of
exact c
o
ntinuation tests
commit
|
commitdiff
|
tree
2020-02-14
Pascal Me
r
z
Fix reading o
f
c
h
eckpoints wi
t
h
P
arrinello-Rahman
.
.
.
commit
|
commitdiff
|
tree
2020-02-14
Pascal
Merz
Fix P
a
rrine
l
l
o-R
a
hman scaling on ini
t
ial step (modular
.
.
.
commit
|
commitdiff
|
tree
2020-02-14
Pas
c
a
l
M
erz
Move modular
s
imu
l
a
tor dec
i
sion before chec
k
p
o
in
t
l
o
ading
commit
|
commitdiff
|
tree
2020-02-13
Pascal Merz
Fix checkNum
b
e
rOfB
o
ndedIntera
c
tion
s
bug
commit
|
commitdiff
|
tree
2020-02-13
Pascal
Merz
Exp
o
s
e vsite counting
commit
|
commitdiff
|
tree
2020-02-05
Pascal Merz
Test Padd
e
d
V
ect
o
r t
o
A
r
rayRe
f
con
v
ersion
commit
|
commitdiff
|
tree
2020-02-05
Pascal
M
erz
Minor imp
r
ovement
s
to vcm
.
cpp
commit
|
commitdiff
|
tree
2020-02-05
P
a
scal Merz
M
e
rge VV
i
mplem
e
ntations of Comput
e
GlobalsElemen
t
commit
|
commitdiff
|
tree
2020-01-31
Pascal Merz
M
o
dular simulator: Allow
for nullptr in
el
e
ment list
.
.
.
commit
|
commitdiff
|
tree
2020-01-31
P
a
scal
Me
r
z
StatePropagator
D
ata: Make co
n
st box getters const f
u
nct
i
o
ns
commit
|
commitdiff
|
tree
2020-01-31
Pascal Merz
Mak
e
t_inputre
c
const in
ComputeGlobalsElement
commit
|
commitdiff
|
tree
2019-12-17
Pascal Me
r
z
Fix ex
a
c
t continuation modular
s
i
mulator
commit
|
commitdiff
|
tree
2019-12-12
Pascal M
e
r
z
Test fo
r
ex
p
ected ou
t
put
files
commit
|
commitdiff
|
tree
2019-12-12
Pa
s
c
a
l Merz
Fix final configu
r
ati
o
n w
r
i
tin
g
fo
r
modula
r
s
imu
l
a
tor
commit
|
commitdiff
|
tree
2019-10-31
Pascal M
e
r
z
Check
f
o
r
contra
d
i
c
ti
n
g environment
v
ari
a
bl
e
s
(modular
.
.
.
commit
|
commitdiff
|
tree
2019-10-30
P
a
scal Merz
Fix doxygen for modular simula
t
o
r
commit
|
commitdiff
|
tree
2019-10-30
P
a
sc
a
l
Merz
Fix
m
od
u
lar s
i
mulator docume
n
tation
commit
|
commitdiff
|
tree
2019-10-29
P
a
scal Merz
Fix compatibility check of modul
a
r si
m
ulator
commit
|
commitdiff
|
tree
2019-10-27
Pascal Merz
En
a
ble forced
rota
t
ion for
m
o
dular simu
l
ator
commit
|
commitdiff
|
tree
2019-10-23
P
asc
a
l
Merz
Cor
r
ect for
s
kewed bo
x
b
efore domai
n
de
c
ompos
i
tion
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
Fix log wr
i
ting (modular
simu
l
ator)
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
Ada
p
t e
n
um
t
o sty
l
e conv
e
nt
i
on (modular
simul
a
to
r
)
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
Sma
l
l improvement
to En
e
rgyElement (mod
u
lar si
m
ulat
o
r
)
commit
|
commitdiff
|
tree
2019-10-22
P
ascal Merz
F
ix stop co
n
dit
i
on
handling
(
modular sim
u
lator)
commit
|
commitdiff
|
tree
2019-10-22
Pasc
a
l
Mer
z
Fix sign
a
l propagatio
n
(
modular simulator)
commit
|
commitdiff
|
tree
2019-10-22
Pascal M
e
r
z
Fix DomDec
s
te
p
(modular
simu
l
ator)
commit
|
commitdiff
|
tree
2019-10-22
Pa
s
cal
Merz
F
ix PmeLoadBa
l
ance
H
e
lper ini
t
ialization (modular simu
l
ato
r
)
commit
|
commitdiff
|
tree
2019-10-01
Pas
c
al Merz
O
u
t
p
u
t correct kinetic at
l
ast step
(
modular
si
m
ulato
r
)
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
Parr
i
nello-Rahman for md-vv
commit
|
commitdiff
|
tree
2019-09-23
Pascal M
e
rz
Parrine
l
lo
-
Rahman baros
t
at fo
r
modular sim
u
lator (leap
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
Pascal Me
r
z
Zer
o
pressure and virial tenso
r
s
a
t beginni
n
g
o
f ste
p
commit
|
commitdiff
|
tree
2019-09-23
Pascal
M
e
rz
Intro
d
uce FEP into m
o
dular
s
imula
t
or
commit
|
commitdiff
|
tree
2019-09-23
P
ascal Merz
Mak
e
CheckpointHelper safer and easier to use
commit
|
commitdiff
|
tree
2019-09-23
Pascal Mer
z
Fix vrescale t
h
ermostat in
t
e
g
ral (modular
simulator)
commit
|
commitdiff
|
tree
2019-09-20
Pas
c
al M
e
rz
Fix r
e
starts in modular si
m
ulator
commit
|
commitdiff
|
tree
2019-09-20
Pascal Me
r
z
Fix domdec
for
md
-
vv m
o
du
l
a
r
simulator
commit
|
commitdiff
|
tree
next