Metadynamics Bug report in colvar: DISTANCE

Ata Roudgar rou... at yahoo.com
Wed Mar 2 22:53:40 CET 2011



On Mar 2, 12:10 pm, Teodoro Laino <teodor... at gmail.com> wrote:
> Dear Ata,
>
> > No Teo, my xj is a fixed point and never change its sign and therefore
> > only xi when it goes far enough it becomes xi --> -xi and therefore
> > (xi-xj) --> (-x1-xj)
>
> sorry this is not the case, since the PBC are applied to the difference xi-xj and not
> to xi and xj independently. See:
>
> > ss=MATMUL(cell%h_inv,xpi-xpj)
>
> anyway.. I try to follow your thoughts:
>
> [..]
>
>
>
>
>
> > now, ss is the transformed version of (Ri-Rj) where Ri=(xi,yi,xi) and
> > Rj=(xj,yj,zj). This is needed because now all ss elements  varied from
> > 0 to 1
> > Now after line 2267
> > ss = ss- NINT (ss)
>
> > the ss remains unchanged if its value changes between 0 to 0.5 that
> > means if the distance between two atoms in x direction does not go
> > betound of half of the length of the unitcell in x direction
> > everything is still fine. The smae for y and z direction. The problem
> > occours when the distance between two atoms (in any direction) goes
> > beyond the half of the length of unit cell (in that direction) in that
> > case
>
> > fist, second or third  element of ss lets say ss = 0.5+\epsilon  after
> > line 2267 the value of ss jump from 0.5+\epsilon to \epsilon because
> > NINT(0.5+x)=x
>
> This is wrong - In fact
>             NINT(0.5+\epsilon) = 1
>             NINT(0.5-\epsilon)=0
> NINT rounds its argument to the nearest whole number.

yes you are right, but it does not change anything you still have jump
at around 0.5 and that is what I mean.


> ======
>
> Let's make a simple 1D example using the equations you have posted. Let's assume you have a 1D cell of 10.
> Your atom (j) is fixed to position 2.
> Your atom (i) is in position 6.
> The difference ss is equal to 4.
>
> After a short time atom (i) continuously moves to position 7.2 -> we know that the distance is now 5.2 if you do not consider periodic boundary conditions.
> Instead, if you consider PBC the real distance is a bit different - In fact, using your notation:
>


exactly, but PBC is not implied on fictitious CV.
The following input file is my metadynamics input file right before
the jump occurs. You can run this input and and look at the file Test-
metadyn-colvar-1.metadynLog. The first column shows the time, second
and third shows the fictitious and actual CV. They should be around
12.4 Bohr. They will always follow each other because the spring
constant in my metadynamics is relatively strong.  After few time step
you will see that the third column jump from 12.875 to 6.469 and
simultaneously the total energy will jump from 463.164 to around
-457.857. If there is no bug in this part of the program please
explain to me why this happens. The ss value right before and after
jump is 0.499 and 0.501. You can choose any cutoff you wish. Please
consider the following input is working for the past 18 ps and there
is no such jump in total energy at all.

Cheers,
Ata

 # Version information for this restart file
 # current date 2011-02-27 17:10:05.108
 # current working dir /global/scratch/aroudgar/metadynamics/at-dcc/
metadynamics/NEW/k-0.3-m-80-w-0.001-YZ/tmp4
 # Program compiled at                              Fri Dec 17
10:47:57 PST 2010
 # Program compiled
on                                                   bugaboo
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x86-64-intel
 # Last CVS
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           2.7133512771225222E-04    4.6531407622418586E-04
5.3971655304983583E-04
          -4.5926517713953160E-04   -5.8339528364184396E-04
1.1106336743747319E-04
           2.5557125698911061E-04   -1.7545768242913388E-03
-2.3471250294436382E-04
           1.6202917735624094E-04   -5.8897834071576808E-04
5.5027483922722451E-04
     &END VELOCITY
     &KIND C
       BASIS_SET DZVP-MOLOPT-GTH
       POTENTIAL GTH-BLYP-q4
       &BASIS
1
2 0 2 7 2 2 1
6.132624767898 -0.105576563700  0.024850587600  0.035098108400
-0.056712999000  0.037469425800
2.625196064782 -0.174866621100  0.147440856000  0.114197930900
-0.076743951500  0.071047574800
1.045456957247  0.064464981400 -0.421418379200  0.215908137300
-0.528056757000  0.619330561200
0.478316330874  0.830447035300  0.823051336800  0.355929151000
0.394594045700  0.710730857000
0.178617414302  0.371911373800  0.184880712100  0.271541842000
0.721247475800  0.389148235000
0.075144725465  0.006174464000 -0.742086051600  0.056256557700
0.733902531700  0.346374124100
0.030286753006  0.008966477300  0.083382192000  0.004998059700
0.248172175500 -0.005142430900
       &END BASIS
       &POTENTIAL
2 2
0.3380660900000000E+00 2 -0.9136268710000000E+01  0.1429259560000000E
+01
2
0.3023222300000000E+00 1  0.9665512280000000E+01
0.2863791200000000E+00 0
       &END POTENTIAL
     &END KIND
     &KIND F
       BASIS_SET DZVP-MOLOPT-GTH
       POTENTIAL GTH-BLYP-q7
       &BASIS
1
2 0 2 7 2 2 1
15.025672765127 -0.076135699000  0.060516471000  0.043030876500
-0.027382614400  0.006095862800
6.156800581515 -0.145492650600  0.078091919900  0.138591822100
-0.119463647500  0.057880784500
2.411456205564  0.195144281500 -0.051537351700  0.283251574300
-0.152089668600  0.143657436500
0.963986369687  0.553654166300 -0.448874166200  0.357678749700
-0.460859710900  0.782158193600
0.396229721431  0.454888028100  0.143111336600  0.300622862100
0.260540362300  0.349204565600
0.157658905678  0.078338198300  0.433345205900  0.138839114100
0.410677921300  0.106634189000
0.048130255107  0.002175323600 -0.111759214900  0.008740274300
0.051656760200 -0.008599668300
       &END BASIS
       &POTENTIAL
2 5
0.2138401400000000E+00 2 -0.2190241518000000E+02  0.3275975720000000E
+01
2
0.1945902800000000E+00 1  0.2379658295000000E+02
0.1878632600000000E+00 0
       &END POTENTIAL
     &END KIND
     &KIND S
       BASIS_SET DZVP-MOLOPT-GTH
       POTENTIAL GTH-BLYP-q6
       &BASIS
1
2 0 2 6 2 2 1
3.817590656735  0.075558928000 -0.045713227100 -0.019219238100
0.001714015800  0.007498037400
2.362751931093 -0.351216488200  0.179094296600 -0.035664835200
0.064608303200  0.104757185100
0.861004180298 -0.099160602500  0.206133423700  0.160834397000
-0.170453754100  0.344818199900
0.417524512433  0.862753116400 -0.737640763800  0.507608206800
-0.536548069500  0.472319101700
0.181513540673  0.307053614900  0.419230078700  0.249563613200
0.786543640200  0.204745694800
0.070570776865  0.001592872500  0.359607313200  0.025974500500
0.740434318200 -0.019952573900
       &END BASIS
       &POTENTIAL
2 4
0.4200000000000000E+00 1 -0.5988800450000000E+01
2
0.3697326600000000E+00 2  0.1255648450000000E+02 -0.3912904590000000E
+01
0.5051538100000000E+01
0.4128757100000000E+00 1  0.3587721140000000E+01
       &END POTENTIAL
     &END KIND
     &KIND O
       BASIS_SET DZVP-MOLOPT-GTH
       POTENTIAL GTH-BLYP-q6
       &BASIS
1
2 0 2 7 2 2 1
12.015954705512 -0.060190841200  0.065738617900  0.036543638800
-0.034210557400  0.014807054400
5.108150287385 -0.129597923300  0.110885902200  0.120927648700
-0.120619770900  0.068186159300
2.048398039874  0.118175889400 -0.053732406400  0.251093670300
-0.213719464600  0.290576499200
0.832381575582  0.462964485000 -0.572670666200  0.352639910300
-0.473674858400  1.063344189500
0.352316246455  0.450353782600  0.186760006700  0.294708645200
0.484848376400  0.307656114200
0.142977330880  0.092715833600  0.387201458600  0.173039869300
0.717465919700  0.318346834400
0.046760918300 -0.000255945800  0.003825849600  0.009726110600
0.032498979400 -0.005771736600
       &END BASIS
       &POTENTIAL
2 4
0.2434202600000000E+00 2 -0.1699189235000000E+02  0.2566142060000000E
+01
2
0.2208314000000000E+00 1  0.1838885102000000E+02
0.2172007000000000E+00 0
       &END POTENTIAL
     &END KIND
     &KIND H
       BASIS_SET DZVP-MOLOPT-GTH
       POTENTIAL GTH-BLYP-q1
       &BASIS
1
2 0 1 7 2 1
11.478000339908  0.024916243200 -0.012512421400  0.024510918200
3.700758562763  0.079825490000 -0.056449071100  0.058140794100
1.446884268432  0.128862675300  0.011242684700  0.444709498500
0.716814589696  0.379448894600 -0.418587548300  0.646207973100
0.247918564176  0.324552432600  0.590363216700  0.803385018200
0.066918004004  0.037148121400  0.438703133000  0.892971208700
0.021708243634 -0.001125195500 -0.059693171300  0.120101316500
       &END BASIS
       &POTENTIAL
1
0.2000000000000000E+00 2 -0.4195961470000000E+01  0.7304982100000000E
+00
0
       &END POTENTIAL
     &END KIND
     &TOPOLOGY
       MULTIPLE_UNIT_CELL               1              1
1
     &END TOPOLOGY
     &COLVAR
       &DISTANCE
         ATOMS               2             19
         AXIS  YZ
       &END DISTANCE
     &END COLVAR
   &END SUBSYS
 &END FORCE_EVAL





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