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Added documentation for shell potentials.
2016-08-24
David
v
an der S
p
oel
A
d
ded documentat
i
on
f
or shell po
t
entials
.
commit
|
commitdiff
|
tree
2016-08-03
David van der Spoel
Three new
q
u
o
tes
.
commit
|
commitdiff
|
tree
2016-07-29
David van der
Spoel
Fixes incorrect charges in OPLS/AA-L
f
o
r HISD and HISE
commit
|
commitdiff
|
tree
2016-07-08
Dav
i
d van de
r
Spoel
Introduce fatal error f
o
r too fe
w
fra
m
es in
gmx dos
.
commit
|
commitdiff
|
tree
2016-06-27
David van de
r
Spoe
l
Made gmx dos w
o
r
k again
.
commit
|
commitdiff
|
tree
2016-06-22
David van der Spoel
Remove
d
s
purious r_ij in force f
o
r
M
orse po
t
ent
i
a
l
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
Davi
d
va
n
der S
p
oel
Modi
f
y lmfit
l
ib
r
ary t
o
avoi
d
clashes with ot
h
er v
e
rsions
.
commit
|
commitdiff
|
tree
2016-03-23
David van
d
e
r
Spoel
Removed srene
w
t
ha
t
was ma
k
ing arr
a
y
s
maller incorrectly
.
commit
|
commitdiff
|
tree
2016-03-18
David van der Spoel
Fixed
d
ivisio
n
by zero i
n
p
o
larize
.
commit
|
commitdiff
|
tree
2016-01-20
David v
a
n
d
er Sp
o
e
l
Couple of new quotes
commit
|
commitdiff
|
tree
2016-01-07
D
a
vid van der Sp
o
el
Ma
d
e no
r
mal m
o
des wo
r
k with shells
and vsites
commit
|
commitdiff
|
tree
2015-11-24
Da
v
id van der Spoel
Fixes newly int
r
oduced bug in make_ndx
.
commit
|
commitdiff
|
tree
2015-11-23
David v
a
n de
r
S
poel
Moved domde
c
stru
c
ture
s
out of commrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David van der S
p
o
el
Cleanups i
n
legacyheader/types
/
commr
e
c
.
h
commit
|
commitdiff
|
tree
2015-11-21
D
a
vid van der S
p
oel
Merge
d
legacyheaders
/
t
y
p
es/q
m
mmrec
.
h in
t
o mdlib/q
m
mm
.
h
commit
|
commitdiff
|
tree
2015-11-21
David v
a
n der Spoel
M
erge
d
g
e
nbor
n
.
h
from lega
c
yheaders/ty
p
es into
mdlib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van
d
er
S
poel
M
oved legacy
h
ead
e
rs/types/group
.
h t
o
mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spo
e
l
Merged legac
y
heade
r
s/
t
ype
s
/
ns
.
h a
n
d
nblist
.
h
t
o
mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
D
a
vid van der S
p
oel
Combine
e
nums
.
h and nam
e
s*
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Merged leg
a
cyheaders/nr
n
b
.
h
an
d
types/nrnb
.
h to gmxlib
.
commit
|
commitdiff
|
tree
2015-11-20
Da
v
id van der Spoel
Moved
mdatom
.
h from
l
egacyheader/types to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
Dav
i
d
van d
e
r Spoel
Moved leg
a
cyheaders/types/energ
y
.
h to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-15
Davi
d
v
an der Spoel
M
erged l
e
gacyheade
r
s/types/inpu
t
rec
.
h in
t
o md
t
y
p
es
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
David
van der
Spoel
M
e
rged legacyhead
e
rs/types/state
.
h i
n
t
o
mdtypes/state
.
h
commit
|
commitdiff
|
tree
2015-11-13
David van der
Spo
e
l
Replaced at
o
m_i
d
by int
.
commit
|
commitdiff
|
tree
2015-11-13
Dav
i
d van der Spoel
Moved genborn
.
h
t
o
m
dli
b
commit
|
commitdiff
|
tree
2015-11-12
David
v
an der
Spoel
Moved txtdump
.
* to fileio
.
commit
|
commitdiff
|
tree
2015-11-12
David
van der Sp
o
el
Mo
v
ed c
o
pyrite
.
*
t
o fileio f
r
o
m gmxlib and leg
a
cyheaders
.
commit
|
commitdiff
|
tree
2015-11-11
Davi
d
v
a
n der Spoel
Moved inputr
e
c
.
* fr
o
m
g
mxlib an
d
lega
c
yheaders to md
t
ypes
.
commit
|
commitdiff
|
tree
2015-11-10
Da
v
id van de
r
S
poel
Removed le
g
acyheaders/typedef
s
.
h
commit
|
commitdiff
|
tree
2015-11-03
David van der S
p
oe
l
Moved
df_hi
s
t
ory utility routines
from
type
d
efs
to
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
David van der Spoel
R
e
placed NOTSET fro
m
t
ypedef
s
.
h by loc
a
l solu
t
ion
s
.
commit
|
commitdiff
|
tree
2015-10-23
David v
a
n der Spoel
R
e
m
o
ved
e
n
e
r
g
yh
i
story code from typede
f
s t
o
a separat
e
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
David
va
n
d
e
r Spoel
M
o
ved pb
c
/cut-off related
u
tilities
fr
o
m
typedefs to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
Dav
i
d van
der Spoel
Freed memo
r
y
i
n legacy statisti
c
s routines
.
commit
|
commitdiff
|
tree
2015-10-03
David van der
S
poel
Removed
s
i
m
p
l
e
.
h
commit
|
commitdiff
|
tree
2015-10-02
David
v
an der Spoel
Removed
simpl
e
.
h from nb_ker
n
el_sse4
_
1_X
X
commit
|
commitdiff
|
tree
2015-10-02
David
van der Spoel
Removed
simple
.
h fr
o
m nb_
k
ernel_ss
e
2_XX
commit
|
commitdiff
|
tree
2015-10-02
D
avid van d
e
r Spoel
R
emoved simple
.
h
from nb_kernel
_
c and nb_
k
ernel_sparc64
_
h
p
c
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
David
v
an der Spoel
R
e
moved inclu
d
e simple
.
h from nb_kernel_avx
_
128_fma
_
XX
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
Remov
e
d
simple
.
h from
nb_kernel_avx
_
2
5
6_
X
X
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
Removed output_env_t, no
w
using gmx_output
_
env_t *
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
Dav
i
d van
d
er Spoe
l
Removed
t
ypes/nr
n
b
.
h from typedefs
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
David van der Spoe
l
Removed t
y
pes/nblist
.
h
and types/nsgr
i
d
.
h fr
o
m typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-30
D
avid van
d
er Spoe
l
Removed types/mdatom
.
h from
t
ypedefs
.
h
commit
|
commitdiff
|
tree
2015-09-29
David
v
an der Spoel
Removed types/inputrec
.
h fro
m
typ
e
defs
.
h
and re
l
eted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
David van der
S
poel
Fixes
b
ug in
the comput
a
t
ion of Coeff
i
cient of Thermal
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
David van der Spoel
Remo
v
ed
t
yp
e
s/for
c
erec
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-25
David van der Spoel
Removed
include
o
f t
y
pe
s
/ifu
n
c
.
h from
typedef
s
.
h
commit
|
commitdiff
|
tree
2015-09-22
Da
v
id van der Spoel
Re
m
oved
four
include
s
from legacyheaders/typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
David van de
r
Spoel
Removed legacyheaders/types/c
o
mmrec_fwd
.
h from typedef
.
h
commit
|
commitdiff
|
tree
2015-09-10
David van
der Spoel
Moved c
o
ntent from
m
drun
.
h
t
o separate headers
.
commit
|
commitdiff
|
tree
2015-09-10
David van der Spoel
Rem
o
ved <sys/types
.
h> and
"
types/constr
.
h
"
from
t
yped
e
fs
commit
|
commitdiff
|
tree
2015-09-09
David van
d
er Spoel
Remov
e
d file
i
o/trx
.
h f
r
o
m
ty
p
e
d
efs
.
h
commit
|
commitdiff
|
tree
2015-09-08
David
van der Spoel
Mov
e
d fun
c
tions operating on
forcere
c
to separate hea
d
er
.
commit
|
commitdiff
|
tree
2015-08-28
D
a
v
i
d van der
Spo
e
l
Added en
e
rg
y
(ed
r
) fil
e
ty
p
e to Optio
n
s
h
e
a
d
e
r
s
.
commit
|
commitdiff
|
tree
2015-08-28
David van der Spoel
Added additio
n
al con
s
tr
u
ctor to StringStream cla
s
s
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
David van der Spoel
Made
output fro
m
dumpin
g
neight
b
orlists ea
s
ier to read
.
commit
|
commitdiff
|
tree
2015-07-31
David van
d
e
r
Spoel
Change ini
t
ial parameters for testing exp
f
i
t
.
commit
|
commitdiff
|
tree
2015-07-29
David van der Spoe
l
Code for checking xv
g
f
iles
i
n testut
i
ls
.
commit
|
commitdiff
|
tree
2015-04-17
David van der
Spoel
Updated exp
o
nential fitting to make i
t
robust
.
commit
|
commitdiff
|
tree
2015-04-09
David van der Spoel
Cla
r
ifi
e
d comments for time-depe
n
dent electr
i
c fields
.
commit
|
commitdiff
|
tree
2015-04-08
D
a
v
id v
a
n der Spoel
Fixed inc
o
r
rec
t
o
ut
p
ut of gb_algo
r
ith as s
a
_
algorithm
.
commit
|
commitdiff
|
tree
2015-03-02
David van de
r
Spoel
Upda
t
ed docu
m
ent
a
tion f
o
r electric fields
.
commit
|
commitdiff
|
tree
2014-12-13
David
v
a
n der Spoel
Fou
r
new quotes from a
r
oun
d
the world
.
commit
|
commitdiff
|
tree
2014-11-28
D
avid van der Spoe
l
Fixes recently
i
ntroduced
b
ug i
n
gmx
a
nalyz
e
.
commit
|
commitdiff
|
tree
2014-11-24
Davi
d
v
an
der Spoe
l
Added war
n
ings
f
o
r ewald-geometry and surface-ep
s
i
lon
commit
|
commitdiff
|
tree
2014-10-28
D
a
vid van
d
er Spoel
Even more refres
h
i
n
g quotes
.
commit
|
commitdiff
|
tree
2014-10-14
David van
d
er Spoe
l
Reorgan
i
zing analysis of cor
r
e
la
t
ion functions
.
commit
|
commitdiff
|
tree
2014-09-23
David v
a
n
der
Spoel
Fix
e
s potential bug in ne
i
gh
b
o
r
searchi
n
g
.
commit
|
commitdiff
|
tree
2014-09-17
Da
v
i
d
van de
r
Spoel
Merge release-
5
-0 into
m
aster
commit
|
commitdiff
|
tree
2014-09-10
David van
d
er Sp
o
e
l
R
e
move
.
tpa,
.
tpb,
.
t
p
x,
.
trj files
.
P
art
o
f #1500
.
commit
|
commitdiff
|
tree
2014-08-30
D
avi
d
van der
S
p
oel
Fixes issue with vs
i
ten an
d
verlet buffers
.
commit
|
commitdiff
|
tree
2014-07-05
David
van
der Sp
o
el
Fixed
inconsistency i
n
bl
o
cka
handling
.
commit
|
commitdiff
|
tree
2014-06-29
David van de
r
Spoel
F
i
xes
#1532, SEGV in g
_
current
.
commit
|
commitdiff
|
tree
2014-06-25
Da
v
id v
a
n der Spo
e
l
Add
e
d check
for
d
omain decomposition and
shells
.
commit
|
commitdiff
|
tree
2014-06-24
D
a
vid van d
e
r Spoel
Added ch
e
ck i
n
grompp for shells
and
i
nputrec issues
.
commit
|
commitdiff
|
tree
2014-06-22
D
a
vid v
a
n der Spoel
Im
p
le
m
ented
fatal error fo
r
nstcalcenergy!=1 with
s
hell
s
.
commit
|
commitdiff
|
tree
2014-06-13
Dav
i
d
van d
e
r Spoel
Fix m
e
mory-usage error in g_chi
commit
|
commitdiff
|
tree
2014-06-11
David van der
S
poel
Fixes bug w
h
ere -
e
and
-d
t
flags
d
id not work anymore
.
commit
|
commitdiff
|
tree
2014-06-07
D
avid van
der Spoel
Merge "Merge
r
e
l
e
ase-5-0 i
n
to
ma
s
t
e
r"
commit
|
commitdiff
|
tree
2014-06-07
D
a
v
i
d
van
d
e
r
Spoel
Me
r
ge rele
a
se-5-0 into master
commit
|
commitdiff
|
tree
2014-06-02
Dav
i
d v
a
n d
e
r Spoel
F
i
xed wrong journ
a
l
r
e
fe
r
ence in
m
anual
commit
|
commitdiff
|
tree
2014-05-31
David v
a
n
der
Spoel
Permit
t
rjc
o
nv to
r
e
ad and
write
v
elocit
i
e
s
with T
N
G
.
.
.
commit
|
commitdiff
|
tree
2014-05-16
Dav
i
d van der Spoel
Fixes a complic
a
t
ed bug in g_anae
i
g
.
commit
|
commitdiff
|
tree
2014-05-15
David van de
r
Spoel
A
d
ded cmak
e
profiling suppor
t
commit
|
commitdiff
|
tree
2014-04-02
Dav
i
d va
n
d
er Spoel
Removed possibility of compiling wit
h
G
SL
.
commit
|
commitdiff
|
tree
2014-03-31
David van der Spo
e
l
Fi
x
ed c
o
m
p
ilation
i
s
s
u
e
in fgrid
.
cpp due to
int/enum
commit
|
commitdiff
|
tree
2014-03-06
David
van
d
er
Spoel
Six new quote
s
fro
m
c
l
assic lite
r
atu
r
e
.
commit
|
commitdiff
|
tree
2014-02-11
David v
a
n der S
p
oel
F
i
xed another vmdio issue
.
commit
|
commitdiff
|
tree
2014-02-10
David van d
e
r Sp
o
el
Mo
v
ed conditiona
l
c
make cod
e
for vmdio
.
commit
|
commitdiff
|
tree
2014-01-28
David va
n
de
r
Spoel
Moved
r
a
ndom nu
m
b
e
r gen
e
rato
r
code
t
o se
p
arate dir
.
commit
|
commitdiff
|
tree
2014-01-18
David v
a
n d
e
r
S
poel
This patch moves
t
he stat
i
stics
l
ibrary
to it
s
own
.
.
.
commit
|
commitdiff
|
tree
2014-01-17
D
avid
v
a
n der Spoel
This patch
moves preprocessing
h
eaders to gmxpreprocess
commit
|
commitdiff
|
tree
2014-01-15
D
a
vi
d
van der Spoel
This
pa
t
ch moves the nrama
.
[ch
]
to
t
he
gmxana dir
.
commit
|
commitdiff
|
tree
2014-01-13
David van der Spoel
Cleaned u
p
li
s
t
o
f GROMACS authors
commit
|
commitdiff
|
tree
2014-01-09
David
van der Sp
o
el
Fixed precisi
o
n in thermal expans
i
o
n
coefficient
c
alc
.
commit
|
commitdiff
|
tree
2013-12-23
David
v
an der
S
poel
Fixe
d
compila
t
i
o
n is
s
u
e
du
e
t
o gcc4
.
8
commit
|
commitdiff
|
tree
2013-12-21
David van der Spoel
More Nobe
l
quot
e
s
a
nd others
commit
|
commitdiff
|
tree
2013-11-07
David van der
S
poel
12
n
ew qu
o
t
e
s
commit
|
commitdiff
|
tree
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