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Clean up vsite code
2016-03-18
Davi
d
van der Spoel
Fixed division by zero in polariz
e
.
commit
|
commitdiff
|
tree
2016-01-20
D
a
v
i
d van der Spo
e
l
Couple of new q
u
otes
commit
|
commitdiff
|
tree
2016-01-07
David van der
S
poel
Mad
e
normal modes
work wit
h
shells and vsites
commit
|
commitdiff
|
tree
2015-11-24
D
a
v
i
d van der Sp
o
el
Fix
e
s newly
i
ntrodu
c
ed bug in mak
e
_ndx
.
commit
|
commitdiff
|
tree
2015-11-23
David
v
an der S
p
oel
Moved
d
omdec st
r
uctures ou
t
o
f
comm
r
ec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David van der S
p
oel
Clea
n
u
ps in legacyheader/types/comm
r
ec
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van der Spoe
l
M
e
rged legacyh
e
aders/types/
q
mmmrec
.
h
in
t
o
mdlib
/
qmm
m
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van der Spoel
Merged genborn
.
h from legacyheaders/types into m
d
lib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David
van
der Spoel
Mo
v
ed
l
e
g
acyhead
e
rs/t
y
pes/group
.
h to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
David van
d
er Spoel
Merg
e
d leg
a
cyheader
s
/t
y
pes/ns
.
h and nblist
.
h to mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Combin
e
enums
.
h and name
s
*
.
commit
|
commitdiff
|
tree
2015-11-20
David
van der Spoel
Me
r
ged legacy
h
eaders/
n
rnb
.
h and types/nrnb
.
h to gm
x
lib
.
commit
|
commitdiff
|
tree
2015-11-20
David van d
e
r Sp
o
e
l
Moved mdatom
.
h f
r
om lega
c
yheader/types to mdtype
s
.
commit
|
commitdiff
|
tree
2015-11-20
David van der
S
poel
Move
d
le
g
a
c
yhe
a
ders/t
y
pes/energy
.
h
t
o mdtypes
.
commit
|
commitdiff
|
tree
2015-11-15
David van der Spoel
M
e
rged le
g
a
c
yhea
d
ers/type
s
/in
p
utrec
.
h
into mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
Davi
d
van
der Spoel
M
e
r
ged
l
egacy
h
ead
e
rs/type
s
/state
.
h
in
t
o mdtyp
e
s
/
state
.
h
commit
|
commitdiff
|
tree
2015-11-13
David van der
Spoel
Replaced ato
m
_id by
i
nt
.
commit
|
commitdiff
|
tree
2015-11-13
David van
d
er Spoe
l
Moved gen
b
or
n
.
h
to m
d
l
i
b
commit
|
commitdiff
|
tree
2015-11-12
David van der
S
po
e
l
Moved txt
d
ump
.
*
to fileio
.
commit
|
commitdiff
|
tree
2015-11-12
Dav
i
d van d
e
r
Spoel
Mo
v
ed copyri
t
e
.
* to
fileio from
g
mxlib and legacyheader
s
.
commit
|
commitdiff
|
tree
2015-11-11
Dav
i
d
v
an
der Spo
e
l
M
o
v
ed input
r
ec
.
* fr
o
m
gmxl
i
b and legacyheaders t
o
mdtype
s
.
commit
|
commitdiff
|
tree
2015-11-10
David van der
S
poel
Remo
v
ed legacyheaders/typedefs
.
h
commit
|
commitdiff
|
tree
2015-11-03
David van der Spoel
Mo
v
e
d
df_hist
o
r
y
utility rou
t
i
n
es
from t
y
pedefs
t
o
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
David van der Spoel
Replac
e
d NO
T
SET from t
y
p
edefs
.
h by local sol
u
tion
s
.
commit
|
commitdiff
|
tree
2015-10-23
D
avid van d
e
r Spoel
R
emove
d
energyhis
t
ory code from typed
e
fs to a separate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
David van
d
er Sp
o
e
l
Moved pbc/c
u
t-off r
e
lat
e
d util
i
ties from
typ
e
defs to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
David van der Spoel
Freed memory in le
g
acy statistics routines
.
commit
|
commitdiff
|
tree
2015-10-03
Da
v
id v
a
n der Spoel
Removed simple
.
h
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
Removed si
m
ple
.
h from nb_kernel_sse4_1_
X
X
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
R
e
m
o
ved sim
p
le
.
h
f
r
om nb_kerne
l
_ss
e
2_XX
commit
|
commitdiff
|
tree
2015-10-02
David van d
e
r Spo
e
l
Removed simpl
e
.
h
f
ro
m
nb_kerne
l
_c
a
nd nb
_
kernel_sparc64_hpc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
David
v
an der Spoe
l
Removed
include simple
.
h
from nb_kerne
l
_avx_
1
28_fma_XX
commit
|
commitdiff
|
tree
2015-10-02
D
avid va
n
der S
p
o
e
l
Removed
s
i
mple
.
h from nb_ke
r
nel_
a
vx_256_XX
commit
|
commitdiff
|
tree
2015-10-02
David
v
an der Sp
o
el
R
em
o
ved out
p
ut_env_t,
n
o
w using gmx_output_env_t
*
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
David van der Spoe
l
R
e
moved types
/
n
r
nb
.
h fro
m
typede
f
s
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
David van
d
e
r
Spoel
Remove
d
types
/
nblist
.
h
an
d
types/nsg
r
id
.
h f
r
o
m
t
y
p
edef
s
.
h
commit
|
commitdiff
|
tree
2015-09-30
David van
d
e
r
Spoel
R
e
moved ty
p
es/mdatom
.
h
from
t
yp
e
defs
.
h
commit
|
commitdiff
|
tree
2015-09-29
David van der
S
poel
R
e
moved types
/
inpu
t
r
e
c
.
h from t
y
pedefs
.
h and rel
e
ted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
D
avid van der Spoel
F
ixe
s
b
ug in the computation of
C
oeffi
c
ient of T
h
ermal
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
D
a
v
id van der
S
poel
R
emoved types
/
forcerec
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-25
David van der S
p
oel
R
emoved include of types/if
u
nc
.
h
from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
David van der Sp
o
el
Remo
v
ed four incl
u
de
s
from
legacyheaders
/
t
y
pedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
D
avid van der Spoel
Removed legacyheaders/types/co
m
mrec
_
fwd
.
h from
typed
e
f
.
h
commit
|
commitdiff
|
tree
2015-09-10
David van der Spoel
Moved content from mdrun
.
h
to separate he
a
ders
.
commit
|
commitdiff
|
tree
2015-09-10
Dav
i
d van der Spoel
Removed <sys/ty
p
e
s
.
h
> an
d
"types/constr
.
h"
f
r
o
m typ
e
defs
commit
|
commitdiff
|
tree
2015-09-09
David van der Spoel
Removed fileio/trx
.
h from
typedef
s
.
h
commit
|
commitdiff
|
tree
2015-09-08
D
a
vi
d
van der Spo
e
l
Mov
e
d functions operatin
g
on fo
r
cerec to s
e
parate
header
.
commit
|
commitdiff
|
tree
2015-08-28
Davi
d
van der
Spoel
Added e
n
ergy (e
d
r) fi
l
e
t
ype to Options
h
e
aders
.
commit
|
commitdiff
|
tree
2015-08-28
Davi
d
van
der Spoel
Ad
d
ed
additional constr
u
cto
r
to
S
trin
g
S
trea
m
c
l
a
ss
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
Davi
d
van der S
p
oel
Made ou
t
put fr
o
m dumpin
g
nei
g
htborlists easier to rea
d
.
commit
|
commitdiff
|
tree
2015-07-31
David van der
Spo
e
l
Change
i
n
i
t
i
a
l
parameters for testing expfi
t
.
commit
|
commitdiff
|
tree
2015-07-29
David van
der Sp
o
el
Code
for checking xvg
files
in t
e
stuti
l
s
.
commit
|
commitdiff
|
tree
2015-04-17
D
avid van
d
er Spoel
Up
d
ated exponenti
a
l fit
t
in
g
to make it robust
.
commit
|
commitdiff
|
tree
2015-04-09
David van der Spo
e
l
Clarified comments for time-d
e
pe
n
d
ent el
e
ctric fi
e
lds
.
commit
|
commitdiff
|
tree
2015-04-08
D
avid
van der Spoel
Fixed in
c
orrect out
p
u
t of gb_algorith as sa_algorithm
.
commit
|
commitdiff
|
tree
2015-03-02
Dav
i
d van d
e
r
Spoel
Updated docum
e
ntation for e
l
ectri
c
fields
.
commit
|
commitdiff
|
tree
2014-12-13
Dav
i
d van der Spoe
l
Fo
u
r new
q
uotes fro
m
a
r
oun
d
the wor
l
d
.
commit
|
commitdiff
|
tree
2014-11-28
Davi
d
v
an der Spoel
Fixes recently
introduce
d
bug
in gmx
anal
y
z
e
.
commit
|
commitdiff
|
tree
2014-11-24
David van der Spoel
Added wa
r
nings for ew
a
ld-geomet
r
y and su
r
face-ep
s
ilon
commit
|
commitdiff
|
tree
2014-10-28
D
avid van der Spoel
E
v
en more
refres
h
ing quotes
.
commit
|
commitdiff
|
tree
2014-10-14
Davi
d
v
a
n
der
Spoel
Reo
r
g
a
nizing a
n
a
lysis of cor
r
elation function
s
.
commit
|
commitdiff
|
tree
2014-09-23
David van der
S
poel
Fixes pot
e
ntial bug in neighborse
a
rching
.
commit
|
commitdiff
|
tree
2014-09-17
David van der Spoel
Merg
e
r
e
lease-5-0 in
t
o master
commit
|
commitdiff
|
tree
2014-09-10
Da
v
id van der Spoel
R
em
o
ve
.
t
pa
,
.
t
pb,
.
t
p
x,
.
trj files
.
Part
of
#15
0
0
.
commit
|
commitdiff
|
tree
2014-08-30
David van der Spoel
Fixe
s
issue wi
t
h vsiten
a
nd v
e
rlet buffers
.
commit
|
commitdiff
|
tree
2014-07-05
David
v
an d
e
r
Spo
e
l
Fixed inconsistency
in
b
locka ha
n
dl
i
n
g
.
commit
|
commitdiff
|
tree
2014-06-29
David van der
S
poel
Fixe
s
#1
5
3
2, S
E
GV in g
_
curren
t
.
commit
|
commitdiff
|
tree
2014-06-25
David
van
d
er Spoel
A
d
ded
ch
e
ck for
d
o
m
ai
n
dec
o
mp
o
sit
i
on and shells
.
commit
|
commitdiff
|
tree
2014-06-24
Dav
i
d van der Spoel
Added che
c
k i
n
g
r
ompp for
s
hells
and inputre
c
issues
.
commit
|
commitdiff
|
tree
2014-06-22
Dav
i
d
v
an der Spoe
l
Implemented fatal erro
r
for
n
s
t
calcenerg
y
!=1 with
s
hells
.
commit
|
commitdiff
|
tree
2014-06-13
David van der Spoel
F
ix memory-usage e
r
ror i
n
g_chi
commit
|
commitdiff
|
tree
2014-06-11
Dav
i
d
van
de
r
S
p
oel
Fixes bug wher
e
-
e and -dt flags did n
o
t work anymore
.
commit
|
commitdiff
|
tree
2014-06-07
David van der Spoel
Merge "Merge release-
5
-0 int
o
master"
commit
|
commitdiff
|
tree
2014-06-07
David va
n
der Spo
e
l
Merg
e
release-5-0 into
m
as
t
er
commit
|
commitdiff
|
tree
2014-06-02
David van der Spoel
Fixed wrong journal reference in m
a
nual
commit
|
commitdiff
|
tree
2014-05-31
D
avid
v
an d
e
r Spoel
Permit
t
r
jc
o
nv to read and writ
e
velocities with T
N
G
.
.
.
commit
|
commitdiff
|
tree
2014-05-16
David van
d
er Sp
o
el
Fix
e
s a complicated bug in g_a
n
a
e
ig
.
commit
|
commitdiff
|
tree
2014-05-15
D
avid
van
der
S
poe
l
Added
c
make
pro
f
iling
support
commit
|
commitdiff
|
tree
2014-04-02
David va
n
der Spoel
Re
m
ove
d
possibility of
c
ompiling with GSL
.
commit
|
commitdiff
|
tree
2014-03-31
David v
a
n der Spoel
F
ixed co
m
p
i
l
ation
i
ssue in f
g
r
i
d
.
cpp due to int/enum
commit
|
commitdiff
|
tree
2014-03-06
Davi
d
van der Spoe
l
Six
new quotes from cl
a
ssic liter
a
ture
.
commit
|
commitdiff
|
tree
2014-02-11
David van der
Spoel
Fixed another vmdio issue
.
commit
|
commitdiff
|
tree
2014-02-10
D
avid van der Spoel
Moved
conditio
n
al cmake code for vmdi
o
.
commit
|
commitdiff
|
tree
2014-01-28
David van der
Spoel
Move
d
random number generator code to separate dir
.
commit
|
commitdiff
|
tree
2014-01-18
David van de
r
Spo
e
l
This patch mo
v
es the statistics library t
o
its own
.
.
.
commit
|
commitdiff
|
tree
2014-01-17
D
a
v
id
v
a
n der Spoel
T
his patch moves preprocessing he
a
d
e
rs to
gmxpreproc
e
ss
commit
|
commitdiff
|
tree
2014-01-15
Davi
d
va
n
der
S
p
oel
T
his patch
m
oves the n
r
ama
.
[ch] to th
e
g
mxana dir
.
commit
|
commitdiff
|
tree
2014-01-13
David v
a
n der Spoel
Cleaned up list o
f
GRO
M
AC
S
author
s
commit
|
commitdiff
|
tree
2014-01-09
David va
n
der Spoel
Fixed precision in thermal expa
n
sion coe
f
fici
e
n
t calc
.
commit
|
commitdiff
|
tree
2013-12-23
David van
der
S
poel
Fixed compilation issue d
u
e to gcc4
.
8
commit
|
commitdiff
|
tree
2013-12-21
David van der Spoel
More Nobel quotes and others
commit
|
commitdiff
|
tree
2013-11-07
David van der Sp
o
e
l
12
new quotes
commit
|
commitdiff
|
tree
2013-09-30
Dav
i
d van de
r
Spoel
Ch
a
nge na
m
e of g
m
xdump to dump and g
m
xcheck to check
commit
|
commitdiff
|
tree
2013-09-29
David v
a
n
der
S
p
oel
F
ixes bug in
p
r
o
cessi
n
g virtual_si
t
esn in grompp
.
commit
|
commitdiff
|
tree
2013-09-26
David van der Spo
e
l
Made
M
W
o
f the V
s
i
te par
t
icle t
y
pe
.
commit
|
commitdiff
|
tree
2013-09-21
David
v
an der Spoel
Moved n
g
mx to C++, re
n
amed it t
o
v
iew
.
commit
|
commitdiff
|
tree
2013-08-30
David van der Spoel
Updat
e
d g_c
l
u
s
ter
commit
|
commitdiff
|
tree
2013-07-24
David
v
an der Spoel
Fixes #13
1
2 u
n
initializ
e
d error in g_
e
nemat
.
commit
|
commitdiff
|
tree
2013-07-17
D
a
vid van der Spoel
A
dded
c
itation to free volume paper
.
commit
|
commitdiff
|
tree
2013-06-14
David van de
r
Spoel
New ana
l
ysis tool to compu
t
e the free volume
a
nd
t
otal
.
.
.
commit
|
commitdiff
|
tree
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