[xcrysden] How to display a whole molecule in unit cell with good connection?

[Tone Kokalj]

On Tue, 2015-10-27 at 16:04 +0200, liyincumt at gmail.com wrote:
> My crystal is a kind of amino acid.  In one unit cell,
> there are two molecules.

The problem is that you did not specify the two molecules in
"contiguous" manner, but instead all your atom-coordinates are
"chopped" inside the [0-1] range. Hence some O and H atoms are
displaced by a lattice vector with respect to a parent molecule.

All you need to do is to shift the "displaced" atoms back by a lattice
vector. Because your coordinates are in crystal units, this means that
you need to subtract by "1" the right coordinate(s). I have moved a few
atoms; compare the attached file with your file. There are few more to
be moved ... look at the structure with xcrysden and you will easily
recognise which atoms needs to be moved (this can be facilitated with
the "Select Atom" button; the displayed ID is the sequential number of
the atom, provided you selected the
"Display->Unit of Repetition->Translational Asymmetric unit" 
display-mode.


Best regards,
-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html

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&CONTROL
                       title = '2015971-Asparticacid'
                 calculation = 'vc-relax'
                restart_mode = 'from_scratch'
                      outdir = '/home/yinli/aspartic_acid/vc-relax/test1' ,
                      wfcdir = '/home/yinli/aspartic_acid/vc-relax/test1' ,
                  pseudo_dir = '/home/yinli/espresso-5.1.1/pseudo/' ,
                      prefix = '2015971-Asparticacid'
               etot_conv_thr = 5.0d-7 ,
               forc_conv_thr = 5.0d-4 ,
                       nstep = 1500
 /
 &SYSTEM
                       ibrav = -12
                   celldm(1) =   9.663114537963445
                   celldm(2) =   1.350523125061113, celldm(3) =   1.484795150092891
                   celldm(5) =  -0.185014881113262
                         nat = 32
                        ntyp = 4
                     ecutwfc = 60
                     ecutrho = 600
                 occupations = 'fixed'
 /
 &ELECTRONS
            electron_maxstep = 200
                    conv_thr = 1.0D-10
              diago_thr_init = 1e-4
                 startingpot = 'atomic'
                 startingwfc = 'atomic'
                 mixing_mode = 'plain'
                 mixing_beta = 0.5
                 mixing_ndim = 8
             diagonalization = 'david'
 /
&IONS
                ion_dynamics = 'bfgs'
 /
&CELL
               cell_dynamics = 'bfgs'
 /
ATOMIC_SPECIES
    H    1.00794  H.blyp-van_ak.UPF 
    C   12.01070  C.blyp-van_ak.UPF 
    N   14.00670  N.blyp-van_ak.UPF 
    O   15.99940  O.blyp-van_ak.UPF 

ATOMIC_POSITIONS crystal
 N     0.858300000000000     0.978000000000000     0.316200000000000
 H     0.029000000000000     0.914000000000000     0.388000000000000
 H     0.810000000000000     0.100000000000000     0.389000000000000
 H     0.900000000000000     0.022000000000000     0.188000000000000
 C     0.634800000000000     0.836000000000000     0.295200000000000
 C     0.560500000000000     0.796000000000000     0.478600000000000
 C     0.715600000000000     0.644000000000000     0.219800000000000
 C     0.793000000000000     0.659000000000000     0.037800000000000
 O     0.749700000000000     0.784000000000000     0.609500000000000
 O     0.318400000000000     0.771000000000000     0.481700000000000
 O     0.002000000000000     0.593000000000000     0.008500000000000
 O     0.612500000000000     0.744000000000000    -0.083900000000000
 H     0.468000000000000     0.898000000000000     0.207000000000000
 H     0.881000000000000     0.578000000000000     0.313000000000000
 H     0.541000000000000     0.556000000000000     0.207000000000000
 H     0.679000000000000     0.750000000000000    -0.203000000000000
 N     0.141700000000000     0.478000000000000     0.683800000000000
 H    -0.029000000000000     0.414000000000000     0.612000000000000
 H     0.190000000000000     0.600000000000000     0.611000000000000
 H     0.100000000000000     0.522000000000000     0.812000000000000
 C     0.365200000000000     0.336000000000000     0.704800000000000
 C     0.439500000000000     0.296000000000000     0.521400000000000
 C     0.284400000000000     0.144000000000000     0.780200000000000
 C     0.207000000000000     0.159000000000000     0.962200000000000
 O     0.250300000000000     0.284000000000000     0.390500000000000
 O     0.681600000000000     0.271000000000000     0.518300000000000
 O     0.998000000000000     0.093000000000000     0.991500000000000
 O     0.387500000000000     0.244000000000000     0.083900000000000
 H     0.532000000000000     0.398000000000000     0.793000000000000
 H     0.119000000000000     0.078000000000000     0.687000000000000
 H     0.459000000000000     0.056000000000000     0.793000000000000
 H     0.321000000000000     0.250000000000000     0.203000000000000

K_POINTS automatic
3  2  2   0 0 0