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Fix duplicate variables parameter.
2020-02-27
Pasc
a
l M
e
rz
L
o
o
sen gmx
a
pi
st
o
psign
a
ler test
commit
|
commitdiff
|
tree
2020-02-27
P
ascal M
e
rz
Use l
e
gac
y
code path f
o
r
t
_gr
a
ph (modular simulator)
commit
|
commitdiff
|
tree
2020-02-27
P
a
scal Mer
z
Extract and expose function to d
e
termine whether mo
l
ecul
e
s
.
.
.
commit
|
commitdiff
|
tree
2020-02-26
Pa
s
cal Merz
Fix constr
a
i
nt
contribution to
dhdl
(
modular simulator)
commit
|
commitdiff
|
tree
2020-02-26
Pasc
a
l Merz
Fix
c
a
lculation of rec
i
p
r
o
cal t
e
rms in rer
u
n
commit
|
commitdiff
|
tree
2020-02-24
Pa
s
cal Merz
Use ArrayRef in com
p
ute_glo
b
als
commit
|
commitdiff
|
tree
2020-02-21
Pascal Merz
Use legac
y
code p
a
th for NMR restraints (modular simulator)
commit
|
commitdiff
|
tree
2020-02-21
Pas
c
al Merz
Co
r
rect for skewe
d
box
in non-DD modular si
m
u
l
ato
r
commit
|
commitdiff
|
tree
2020-02-14
P
a
s
c
al Merz
Expand test cover
a
g
e
o
f
exac
t
continuati
o
n tests
commit
|
commitdiff
|
tree
2020-02-14
P
a
scal
Merz
F
i
x r
e
ading o
f
checkpoints with Parr
i
nello-Rahma
n
.
.
.
commit
|
commitdiff
|
tree
2020-02-14
P
a
scal
Merz
F
ix Parr
i
n
ello-Rahman sca
l
ing
on
i
nitial step (
m
odular
.
.
.
commit
|
commitdiff
|
tree
2020-02-14
P
ascal
M
e
rz
Move modular simulator
d
e
c
i
s
ion be
f
ore
c
h
eckpoi
n
t lo
a
ding
commit
|
commitdiff
|
tree
2020-02-13
Pascal Merz
Fix checkNumberOfBonded
I
nteractions
bu
g
commit
|
commitdiff
|
tree
2020-02-13
Pascal M
e
r
z
E
x
pose vsite counting
commit
|
commitdiff
|
tree
2020-02-05
Pascal Merz
T
e
st PaddedV
e
ctor to Ar
r
a
yRef conversion
commit
|
commitdiff
|
tree
2020-02-05
Pasc
a
l
Merz
Min
o
r
i
mp
r
ovements to vcm
.
c
p
p
commit
|
commitdiff
|
tree
2020-02-05
Pascal
Merz
M
e
rge VV
i
mplement
a
tions
o
f
C
omputeGlobalsElement
commit
|
commitdiff
|
tree
2020-01-31
Pa
s
cal Merz
Modular simula
t
or: Allow for n
u
l
l
ptr
i
n element list
.
.
.
commit
|
commitdiff
|
tree
2020-01-31
P
asca
l
Merz
S
t
a
tePropagatorDa
t
a: Make const box getter
s
co
n
st fu
n
ctions
commit
|
commitdiff
|
tree
2020-01-31
Pas
c
al
M
e
rz
Make t_in
p
utrec const
in Com
p
u
t
eGlobalsEl
e
ment
commit
|
commitdiff
|
tree
2019-12-17
Pas
c
al Merz
Fi
x
exact continua
t
ion
m
odular simula
t
or
commit
|
commitdiff
|
tree
2019-12-12
Pascal M
e
rz
Test for expec
t
ed out
p
u
t
f
i
les
commit
|
commitdiff
|
tree
2019-12-12
P
a
sc
a
l Merz
Fix final con
f
i
g
u
ration writing fo
r
modular simulator
commit
|
commitdiff
|
tree
2019-10-31
Pasca
l
Merz
C
heck for contrad
i
cting envi
r
onment
v
ariables
(
modular
.
.
.
commit
|
commitdiff
|
tree
2019-10-30
Pascal
Merz
Fix doxygen for modular simu
l
ator
commit
|
commitdiff
|
tree
2019-10-30
Pascal M
e
rz
F
i
x modular simulator documentation
commit
|
commitdiff
|
tree
2019-10-29
Pascal Merz
Fix compatibili
t
y check
o
f m
o
dul
a
r simulato
r
commit
|
commitdiff
|
tree
2019-10-27
Pascal
M
erz
En
a
ble forced
rotatio
n
f
o
r m
o
d
u
l
ar s
i
mulator
commit
|
commitdiff
|
tree
2019-10-23
Pas
c
al M
e
rz
Co
r
rect for skewed box bef
o
re domain decomposition
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
Pascal
M
erz
Fix lo
g
writing (modular simulator)
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
Adapt enum to style conv
e
ntion (m
o
dular simulator)
commit
|
commitdiff
|
tree
2019-10-23
Pa
s
cal
Merz
Small improvement
to
Ene
r
g
y
Element (mo
d
ular si
m
ulator)
commit
|
commitdiff
|
tree
2019-10-22
Pascal Merz
Fix sto
p
cond
i
tio
n
handling (modula
r
s
imulator)
commit
|
commitdiff
|
tree
2019-10-22
Pascal Merz
F
i
x
s
ignal propagation (
m
o
d
ular simulato
r
)
commit
|
commitdiff
|
tree
2019-10-22
Pascal Merz
Fix DomDec step
(modular
s
i
m
u
lator)
commit
|
commitdiff
|
tree
2019-10-22
Pascal Merz
Fix
P
meLoadBala
n
ceHel
p
er
i
nitia
l
iz
a
tion (modular simulator)
commit
|
commitdiff
|
tree
2019-10-01
Pascal Merz
Output cor
r
e
c
t kinetic
a
t last
s
tep
(mo
d
ula
r
simulato
r
)
commit
|
commitdiff
|
tree
2019-09-23
Pascal
Merz
Parri
n
ello-Rah
m
an
f
or
m
d-v
v
commit
|
commitdiff
|
tree
2019-09-23
Pa
s
cal Merz
Parrinello-Rahm
a
n barostat for mo
d
ular
s
imul
a
t
o
r (leap
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
Zero
pres
s
ure and virial tensors at b
e
g
inni
n
g of step
commit
|
commitdiff
|
tree
2019-09-23
Pas
c
al Mer
z
Int
r
odu
c
e FEP into mod
u
lar simulato
r
commit
|
commitdiff
|
tree
2019-09-23
P
ascal Merz
Make C
h
eckpointHelper safer and e
a
s
ier to use
commit
|
commitdiff
|
tree
2019-09-23
Pa
s
cal Merz
Fix vr
e
scale
t
hermostat inte
g
ral
(
m
o
d
ular simulator
)
commit
|
commitdiff
|
tree
2019-09-20
Pascal
M
e
rz
Fix restart
s
in modular simu
l
ato
r
commit
|
commitdiff
|
tree
2019-09-20
Pascal Merz
Fix domdec for md-vv m
o
d
ul
a
r simulator
commit
|
commitdiff
|
tree
2019-09-20
Pasca
l
Merz
Run
s
imulator equiva
l
ence t
e
s
ts
i
n dou
b
le precision
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Pascal Merz
v-r
e
scale thermostat for modul
a
r si
m
ulator
commit
|
commitdiff
|
tree
2019-09-17
P
ascal
M
erz
M
inor tw
e
aks to
s
um
_
dhdl an
d
set
C
urrentLamb
d
asLocal
commit
|
commitdiff
|
tree
2019-09-17
Pasca
l
Merz
Fix p
o
si
t
ion pinning
f
or mo
d
ul
a
r simulat
o
r
commit
|
commitdiff
|
tree
2019-09-17
Pascal Me
r
z
Fix m
o
dular simulator MPI bugs
commit
|
commitdiff
|
tree
2019-09-17
Pasca
l
Merz
M
a
ke modu
l
ar
s
imulator
th
e
defa
u
l
t
c
o
de path for md
.
.
.
commit
|
commitdiff
|
tree
2019-09-17
Pascal Merz
Fix force element
commit
|
commitdiff
|
tree
2019-09-17
Pascal Merz
Enable
c
h
eckp
o
inti
n
g for m
o
dular simulat
o
r
commit
|
commitdiff
|
tree
2019-09-15
Pa
s
c
al
M
er
z
Introduce the mo
d
ul
a
r simulator
commit
|
commitdiff
|
tree
2019-09-12
Pascal
Merz
U
p
date m
o
dular simulator tests
commit
|
commitdiff
|
tree
2019-09-10
Pascal Merz
CompositeSimulatorE
l
ement fo
r
the mod
u
lar sim
u
la
t
or
commit
|
commitdiff
|
tree
2019-09-10
Pascal Mer
z
Coordinate Pr
o
p
a
gators
commit
|
commitdiff
|
tree
2019-09-10
Pasc
a
l Merz
StatePropagatorData: Introduced cons
t
box acce
s
sor
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Pa
s
cal Me
r
z
Add trivial const
q
ualifiers to shell
f
c a
n
d EnergyOutpu
t
commit
|
commitdiff
|
tree
2019-09-10
P
a
s
cal Merz
C
onstraint eleme
n
t for
the modular simu
l
a
tor
commit
|
commitdiff
|
tree
2019-09-09
Pascal Merz
D
omain decomposi
t
ion and
P
M
E
load ba
l
ancing for modular
.
.
.
commit
|
commitdiff
|
tree
2019-09-07
P
ascal Merz
Ma
k
e pme_loadbal
_
d
o
(
) inde
p
endent of t_sta
t
e
commit
|
commitdiff
|
tree
2019-09-07
Pascal Merz
Forc
e
Elem
e
nt
and ShellFCElem
e
nt fo
r
the modular simulat
o
r
commit
|
commitdiff
|
tree
2019-09-06
Pascal Merz
Co
m
put
e
GlobalsEl
e
ment for the modular simulat
o
r
commit
|
commitdiff
|
tree
2019-09-05
Pascal Merz
Introduce
topolog
y
c
l
ass for modul
a
r simulator
commit
|
commitdiff
|
tree
2019-09-05
P
a
scal M
e
rz
Renam
e
MicroState to StatePropagatorDa
t
a f
o
r m
o
dular
.
.
.
commit
|
commitdiff
|
tree
2019-09-05
Pasca
l
M
e
r
z
Adapt inhe
r
it
a
n
ce inte
n
dation to uncru
s
tify
commit
|
commitdiff
|
tree
2019-09-05
Pascal Merz
Make do_con
s
train_first() independent
o
f t_
s
tate
commit
|
commitdiff
|
tree
2019-09-03
Pas
c
a
l
M
e
r
z
I
n
tro
d
uce en
e
r
g
y e
l
eme
n
t f
o
r mo
d
u
l
ar simulator
commit
|
commitdiff
|
tree
2019-08-28
Pascal Merz
In
t
rod
u
c
e MicroState for modular
s
imulator
commit
|
commitdiff
|
tree
2019-08-28
Pascal Mer
z
Introd
u
c
e signa
l
l
e
rs for modular integrator
commit
|
commitdiff
|
tree
2019-08-28
Pascal Merz
Introduc
e
t
h
e
ma
i
n modular s
i
m
u
lator interfac
e
s and
.
.
.
commit
|
commitdiff
|
tree
2019-08-12
Pa
s
cal Merz
Use new setenv fu
n
ctio
n
for ene
r
gyoutput test
commit
|
commitdiff
|
tree
2019-08-05
Pa
s
cal
M
erz
Add t
r
ivia
l
con
s
t
quali
f
ie
r
t
o
energy output
commit
|
commitdiff
|
tree
2019-08-05
P
a
s
c
al Merz
Add co
n
st
g
etter to MDAtoms
commit
|
commitdiff
|
tree
2019-08-05
Pascal
Mer
z
Move owne
r
ship o
f
k
i
netic energy
object to I
S
im
u
lator
commit
|
commitdiff
|
tree
2019-08-05
P
ascal Merz
Added Simulator
c
omparison test
commit
|
commitdiff
|
tree
2019-08-05
Pascal Merz
Introduce Simul
a
torBuilder
commit
|
commitdiff
|
tree
2019-08-02
Pascal Merz
Introduc
e
Simula
t
or
bas
e
c
lass
commit
|
commitdiff
|
tree
2019-07-31
P
ascal M
e
r
z
R
e
name Simu
l
a
tor t
o
L
e
gacySimula
t
o
r
commit
|
commitdiff
|
tree
2019-07-11
Pas
c
a
l Me
r
z
Get rid of clang-tidy wa
r
ning in do_m
d
/r
e
r
un/m
i
mic
commit
|
commitdiff
|
tree
2019-07-11
Pasc
a
l Merz
Remove dependence of compute_globals on t_state
commit
|
commitdiff
|
tree
2019-07-11
P
a
scal Merz
Make r
e
lax_shell_flexcon indep
e
ndent
of t_state
commit
|
commitdiff
|
tree
2019-07-09
Pascal Merz
Added triv
i
al const quali
f
i
er to
relax_shell_flexco
n
()
commit
|
commitdiff
|
tree
2019-07-09
P
a
scal Merz
Const q
u
alifier for fo
r
ces in update_co
o
rds
commit
|
commitdiff
|
tree
2019-07-01
Pas
c
al Merz
Fix module
d
etection fo
r
phy
s
ical validatio
n
commit
|
commitdiff
|
tree
2019-06-24
P
ascal Merz
Ma
k
e global topology constant
i
n traject
o
ry writing
commit
|
commitdiff
|
tree
2019-05-27
Pasca
l
Merz
Clean up renamed simu
l
ator
.
h
file
commit
|
commitdiff
|
tree
2019-05-25
Pascal Merz
R
e
mo
v
e dependen
c
e
o
f mdoutf
_
write
_
t
o_traject
o
ry_files
.
.
.
commit
|
commitdiff
|
tree
2019-05-25
P
ascal Mer
z
R
e
n
a
me Integrato
r
class
commit
|
commitdiff
|
tree
2019-05-16
P
as
c
al Me
r
z
Use P
y
thon 3
commit
|
commitdiff
|
tree
2018-12-10
Pascal Merz
Failproof
s
i
gna
l
convers
i
o
n
commit
|
commitdiff
|
tree
2018-09-26
P
a
scal Mer
z
(Re-
)
f
ix typo in DD load bala
n
cing printing
commit
|
commitdiff
|
tree
2018-09-25
Pascal Merz
Remove obsolete braces in do_md()
commit
|
commitdiff
|
tree
2018-09-25
Pascal
M
er
z
Rem
o
ve rerun fr
o
m do_md
commit
|
commitdiff
|
tree
2018-09-25
Pasca
l
Merz
Re
m
o
v
e u
n
necessary f
u
nctio
n
ality from do_re
r
u
n
commit
|
commitdiff
|
tree
2018-09-25
P
a
scal Merz
Prepare reru
n
co
m
mit
commit
|
commitdiff
|
tree
2018-09-21
Pascal Merz
Make C
G
L
O_CHECK_NUMBER_OF_BONDED_INTER
A
CTIONS
require
.
.
.
commit
|
commitdiff
|
tree
2018-09-18
Pascal Merz
Docu
m
entation
fix: Reru
n
and nstlis
t
commit
|
commitdiff
|
tree
2018-09-18
Pascal Merz
Introduce stop
h
andler
commit
|
commitdiff
|
tree
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