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Merge branch release-2019 into release-2020
2019-10-31
Pasca
l
Merz
C
h
eck for co
n
t
r
adicting e
n
v
ironment v
a
r
i
a
bl
e
s (modula
r
.
.
.
commit
|
commitdiff
|
tree
2019-10-30
P
a
scal Merz
Fix doxygen for
modular si
m
ulator
commit
|
commitdiff
|
tree
2019-10-30
Pascal Merz
Fix mo
d
ula
r
sim
u
la
t
or docume
n
tation
commit
|
commitdiff
|
tree
2019-10-29
Pascal Merz
F
ix
c
om
p
atibility check of modular simulator
commit
|
commitdiff
|
tree
2019-10-27
Pascal Merz
E
n
able
f
or
c
ed rotation for modular simula
t
o
r
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
Cor
r
ect for skewed
box be
f
o
re domain decom
p
o
s
i
tion
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
Fix log writing (modular simula
t
or)
commit
|
commitdiff
|
tree
2019-10-23
Pasc
a
l Merz
Adapt enum to style con
v
ention (
m
odular sim
u
lator)
commit
|
commitdiff
|
tree
2019-10-23
Pascal
Merz
Small improv
e
ment to
Energy
E
lem
e
nt (modular simulator
)
commit
|
commitdiff
|
tree
2019-10-22
Pascal Merz
Fix
s
top cond
i
tion handlin
g
(mo
d
u
l
ar simulator)
commit
|
commitdiff
|
tree
2019-10-22
Pascal Mer
z
Fix
sign
a
l
propagatio
n
(
m
o
d
ular simul
a
tor)
commit
|
commitdiff
|
tree
2019-10-22
Pasca
l
M
erz
Fix Do
m
Dec step (mod
u
lar simulator)
commit
|
commitdiff
|
tree
2019-10-22
Pasc
a
l Merz
Fix Pm
e
L
oa
d
Ba
l
anceHelper init
i
alization (modu
l
ar simulator
)
commit
|
commitdiff
|
tree
2019-10-01
Pasca
l
Merz
Out
p
u
t
correct kin
e
tic at l
a
st step (mo
d
ular si
m
ula
t
or)
commit
|
commitdiff
|
tree
2019-09-23
P
ascal Me
r
z
Parr
i
nello-Rahm
a
n for md-vv
commit
|
commitdiff
|
tree
2019-09-23
Pas
c
al Merz
Parrinello
-
Rahman barostat for
m
odular simulator (leap
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
Zero pressure
and virial
t
ensors a
t
beginnin
g
of step
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
Introduc
e
FEP into modular si
m
ulato
r
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
Ma
k
e Che
c
kpointHelp
e
r safer and easier to use
commit
|
commitdiff
|
tree
2019-09-23
Pascal
M
erz
Fix vrescale thermostat integral (modular simulator)
commit
|
commitdiff
|
tree
2019-09-20
P
a
s
c
a
l
Merz
Fix
rest
a
rts
in modu
l
ar simul
a
to
r
commit
|
commitdiff
|
tree
2019-09-20
Pascal M
e
rz
F
ix domdec for md-v
v
modular simulato
r
commit
|
commitdiff
|
tree
2019-09-20
P
ascal Merz
Run simulat
o
r equi
v
alence tests in do
u
b
le precision
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Pascal
M
erz
v-r
e
sc
a
le thermo
s
t
at for modu
l
a
r
simula
t
or
commit
|
commitdiff
|
tree
2019-09-17
P
ascal Merz
Minor
tweak
s
to sum_d
h
dl and
s
e
tCurrentLambdasLoca
l
commit
|
commitdiff
|
tree
2019-09-17
P
asc
a
l
Merz
Fix p
o
sition pinning for mod
u
lar
s
i
mulator
commit
|
commitdiff
|
tree
2019-09-17
Pasc
a
l Merz
F
i
x
modul
a
r simulator M
P
I bugs
commit
|
commitdiff
|
tree
2019-09-17
Pascal Mer
z
Make mod
u
lar sim
u
lator the de
f
aul
t
c
o
d
e
path for
m
d
.
.
.
commit
|
commitdiff
|
tree
2019-09-17
Pascal Merz
Fix f
o
rce element
commit
|
commitdiff
|
tree
2019-09-17
Pasca
l
Merz
Enable c
h
eckpointin
g
for modular simula
t
or
commit
|
commitdiff
|
tree
2019-09-15
Pascal Merz
In
t
roduce the modula
r
si
m
u
lator
commit
|
commitdiff
|
tree
2019-09-12
Pascal
Merz
Update modular simu
l
ator tests
commit
|
commitdiff
|
tree
2019-09-10
Pascal Me
r
z
CompositeSimulatorElement for the mo
d
ular
s
imulator
commit
|
commitdiff
|
tree
2019-09-10
Pascal
M
erz
Coo
r
di
n
ate
P
ropaga
t
or
s
commit
|
commitdiff
|
tree
2019-09-10
Pascal Merz
StatePropagatorDat
a
:
Introduce
d
const
box accesso
r
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Pascal
M
e
r
z
Add trivial const qualifiers to
s
hellf
c
and
E
n
ergyOutput
commit
|
commitdiff
|
tree
2019-09-10
Pascal
Merz
Constraint element
for the modular simulator
commit
|
commitdiff
|
tree
2019-09-09
Pasc
a
l Merz
Dom
a
in
d
ecomposition
and PME load bal
a
ncing for m
o
dular
.
.
.
commit
|
commitdiff
|
tree
2019-09-07
Pa
s
cal Merz
Make pme_
l
oadbal_do() independent of t_st
a
te
commit
|
commitdiff
|
tree
2019-09-07
P
as
c
al
Merz
ForceE
l
ement and ShellFCElem
e
nt for the modular simulator
commit
|
commitdiff
|
tree
2019-09-06
Pascal Merz
ComputeGlobalsElement for the modular sim
u
l
a
tor
commit
|
commitdiff
|
tree
2019-09-05
P
a
sc
a
l Merz
Introduce topology class for
m
odular
s
im
u
lator
commit
|
commitdiff
|
tree
2019-09-05
Pascal Merz
Rename MicroSta
t
e to
StateProp
a
gatorData for modul
a
r
.
.
.
commit
|
commitdiff
|
tree
2019-09-05
P
ascal Merz
Adap
t
inheritance intendation to unc
r
u
s
tif
y
commit
|
commitdiff
|
tree
2019-09-05
Pasc
a
l
Merz
Make do_constrain_fi
r
s
t
() indepen
d
ent
o
f
t_s
t
ate
commit
|
commitdiff
|
tree
2019-09-03
P
ascal Merz
Introduce energy element
f
o
r modular simu
l
ator
commit
|
commitdiff
|
tree
2019-08-28
Pasc
a
l Merz
Introdu
c
e MicroStat
e
for modular simulator
commit
|
commitdiff
|
tree
2019-08-28
Pascal Merz
Introduce signal
l
ers
f
or mo
d
ular integrator
commit
|
commitdiff
|
tree
2019-08-28
Pascal
M
e
rz
Introduce
t
h
e m
a
in mod
u
lar s
i
mul
a
tor interfaces
a
n
d
.
.
.
commit
|
commitdiff
|
tree
2019-08-12
Pascal Merz
Use
new
s
etenv function
f
or energyoutput tes
t
commit
|
commitdiff
|
tree
2019-08-05
P
a
scal Merz
Add
t
rivia
l
const qu
a
lifie
r
to energy output
commit
|
commitdiff
|
tree
2019-08-05
Pascal Me
r
z
Add const gett
e
r to MDAtom
s
commit
|
commitdiff
|
tree
2019-08-05
Pascal Merz
Move ownership of kinetic energy object to
I
Simulator
commit
|
commitdiff
|
tree
2019-08-05
Pascal Merz
Add
e
d
S
imul
a
tor comparison test
commit
|
commitdiff
|
tree
2019-08-05
Pasc
a
l Merz
Intr
o
duce Simula
t
orB
u
il
d
er
commit
|
commitdiff
|
tree
2019-08-02
Pas
c
al
Merz
Introduce Simulator base class
commit
|
commitdiff
|
tree
2019-07-31
Pascal
M
erz
Ren
a
me Simul
a
tor t
o
LegacySimulator
commit
|
commitdiff
|
tree
2019-07-11
P
a
s
c
a
l
M
e
r
z
Ge
t
r
i
d of clang-tid
y
warning i
n
do_md/reru
n
/mimic
commit
|
commitdiff
|
tree
2019-07-11
Pascal Merz
R
emove
d
ependence of co
m
p
ut
e
_globals on t
_
state
commit
|
commitdiff
|
tree
2019-07-11
Pascal Merz
Make relax
_
shell_flexcon independen
t
of t_state
commit
|
commitdiff
|
tree
2019-07-09
Pascal Merz
Added
tr
i
vial const qualifier
t
o
r
e
lax_s
h
ell_flexcon
(
)
commit
|
commitdiff
|
tree
2019-07-09
Pas
c
al
M
erz
C
onst q
u
alifier for forces in update_c
o
o
rds
commit
|
commitdiff
|
tree
2019-07-01
Pasc
a
l
Merz
Fix modul
e
detection
for
p
hysic
a
l val
i
d
a
tion
commit
|
commitdiff
|
tree
2019-06-24
P
ascal Merz
M
a
ke g
l
obal topology consta
n
t in traject
o
r
y
w
r
iting
commit
|
commitdiff
|
tree
2019-05-27
Pasc
a
l
Merz
Clean up re
n
amed simulator
.
h file
commit
|
commitdiff
|
tree
2019-05-25
Pascal Merz
Re
m
o
ve
d
epe
n
d
e
n
ce of m
d
outf
_
w
r
ite_to_trajec
t
ory_file
s
.
.
.
commit
|
commitdiff
|
tree
2019-05-25
P
a
s
c
al Merz
Rename In
t
egrator class
commit
|
commitdiff
|
tree
2019-05-16
Pasc
a
l Merz
Use Python 3
commit
|
commitdiff
|
tree
2018-12-10
Pascal Me
r
z
Failproof
s
i
g
nal conversi
o
n
commit
|
commitdiff
|
tree
2018-09-26
Pascal Merz
(Re-)fix typo in
D
D
lo
a
d
b
alan
c
ing printing
commit
|
commitdiff
|
tree
2018-09-25
Pascal M
e
rz
Remove obso
l
ete b
r
aces in do_md()
commit
|
commitdiff
|
tree
2018-09-25
P
a
scal Me
r
z
Remove r
e
run from
d
o
_
md
commit
|
commitdiff
|
tree
2018-09-25
Pascal Merz
Remove unnecess
a
r
y
f
unctiona
l
ity from
d
o
_
rerun
commit
|
commitdiff
|
tree
2018-09-25
Pa
s
cal Merz
P
repare
rerun commit
commit
|
commitdiff
|
tree
2018-09-21
Pa
s
cal Merz
Make CGLO_
C
HECK_NUMBER_OF_BONDED_INTERACTIONS re
q
uire
.
.
.
commit
|
commitdiff
|
tree
2018-09-18
Pascal
M
erz
D
o
cumen
t
ation fix
:
Rerun an
d
nstlist
commit
|
commitdiff
|
tree
2018-09-18
P
a
scal Me
r
z
Introduce
stop handler
commit
|
commitdiff
|
tree
2018-09-18
Pasca
l
Merz
Int
r
oduce che
c
kpoint h
a
nd
l
er
commit
|
commitdiff
|
tree
2018-09-18
Pas
c
a
l Merz
Introduce reset
h
a
ndler
commit
|
commitdiff
|
tree
2018-09-17
Pascal Merz
F
ix t
y
po
i
n
D
D load
b
alancing print
i
ng
commit
|
commitdiff
|
tree
2018-09-11
P
a
scal
Merz
Adde
d
trivial con
s
t
qualifiers
commit
|
commitdiff
|
tree
2018-09-11
P
asca
l
Merz
In
i
t
i
alize to
t
a
l_vir and pres in init_m
d
commit
|
commitdiff
|
tree
2018-04-04
Pascal Merz
Mo
v
e checkNumberOfBondedInt
e
ractions
commit
|
commitdiff
|
tree
2017-12-21
Pascal Me
r
z
Doc
u
ment
a
tio
n
and fixes
f
or physical va
l
idation
commit
|
commitdiff
|
tree
2017-11-22
P
a
sca
l
Me
r
z
Proof of concept: P
h
ysi
c
al val
i
d
ation suite
commit
|
commitdiff
|
tree