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

[liyincumt at gmail.com]

Dear Matic, 

Thanks for your patient explanation!
There are only two very small negative values in the final coordinates. My crystal is a kind of amino acid.  In one unit cell, there are two molecules. In my input file, there is no negative values in atomic coordinates, but the boundary still can apparently break the chemical bonds.

Input:
&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     0.916100000000000
 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     0.797000000000000
 N     0.141700000000000     0.478000000000000     0.683800000000000
 H     0.971000000000000     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



Dr. Yin Li 
Department of Biophysics,Medical School, University of Pecs,
No.12 Szigeti Street, Pecs, H-7624, HUNGARY
Phone: +36-72-535271/36271

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