[Pw_forum] "nat_todo",could anyone help me?
Elham
e.chemistry83 at gmail.com
Thu Jul 16 13:07:44 CEST 2015
Dear all,
I want to do phonon calculation on an adsorption system.
I did a test calculation on a system, an molecule is adsorbed on a surface.
I just want to calculate the vibration frequencies of the molecule and
surrounding atom on the surface (19 atom). I set "nat_todo" in the input
file of ph.x, and set the list of indices of atoms of the molecule (5 6 10
35 38 42 44 45 49 50 55 56 57 58 59 60 61 62 63). But in the result file
phonons for all atoms and some of frequencies negative and some frequencies
positive. . I don't know what's wrong with it, and how to set parameter
in the input file of ph.x. Please help me! Thank you!
A lot of negative frequencies because of surface atoms and molecules
binding to each other this happen?
Atomic displacements:
There are 189 irreducible representations
Representation 1 1 modes -A Not done in this run
Representation 2 1 modes -A Not done in this run
Representation 3 1 modes -A Not done in this run
Representation 4 1 modes -A Not done in this run
Representation 5 1 modes -A Not done in this run
Representation 6 1 modes -A Not done in this run
Representation 7 1 modes -A Not done in this run
Representation 8 1 modes -A Not done in this run
Representation 9 1 modes -A Not done in this run
Representation 10 1 modes -A Not done in this run
Representation 11 1 modes -A Not done in this run
Representation 12 1 modes -A Not done in this run
Representation 13 1 modes -A Done (for atom 5)
And in the output phonon list of frequencies: \
freq ( 1 - 1) = -576.0 [cm-1] --> A I+R
freq ( 2 - 2) = -573.5 [cm-1] --> A I+R
freq ( 3 - 3) = -570.6 [cm-1] --> A I+R
freq ( 4 - 4) = -560.4 [cm-1] --> A I+R
freq ( 5 - 5) = -517.5 [cm-1] --> A I+R
freq ( 6 - 6) = -515.5 [cm-1] --> A I+R
freq ( 7 - 7) = -482.4 [cm-1] --> A I+R
freq ( 8 - 8) = -471.4 [cm-1] --> A I+R
freq ( 9 - 9) = -462.6 [cm-1] --> A I+R
freq ( 10 - 10) = -460.7 [cm-1] --> A I+R
freq ( 11 - 11) = -369.1 [cm-1] --> A I+R
freq ( 12 - 12) = -358.2 [cm-1] --> A I+R
freq ( 13 - 13) = -332.7 [cm-1] --> A I+R
freq ( 14 - 14) = -327.7 [cm-1] --> A I+R
freq ( 15 - 15) = -275.8 [cm-1] --> A I+R
freq ( 16 - 16) = -271.7 [cm-1] --> A I+R
freq ( 17 - 17) = -268.3 [cm-1] --> A I+R
freq ( 18 - 18) = -262.7 [cm-1] --> A I+R
freq ( 19 - 19) = -255.8 [cm-1] --> A I+R
freq ( 20 - 20) = -251.8 [cm-1] --> A I+R
freq ( 21 - 21) = -246.1 [cm-1] --> A I+R
freq ( 22 - 22) = -234.3 [cm-1] --> A I+R
freq ( 23 - 23) = -221.0 [cm-1] --> A I+R
freq ( 24 - 24) = -215.0 [cm-1] --> A I+R
freq ( 25 - 25) = -204.2 [cm-1] --> A I+R
freq ( 26 - 26) = -195.2 [cm-1] --> A I+R
freq ( 27 - 27) = -187.3 [cm-1] --> A I+R
freq ( 28 - 28) = -186.7 [cm-1] --> A I+R
freq ( 29 - 29) = -171.3 [cm-1] --> A I+R
freq ( 30 - 30) = -146.4 [cm-1] --> A I+R
freq ( 31 - 31) = -94.0 [cm-1] --> A I+R
freq ( 32 - 32) = -93.1 [cm-1] --> A I+R
freq ( 33 - 33) = -89.9 [cm-1] --> A I+R
freq ( 34 - 34) = -87.6 [cm-1] --> A I+R
freq ( 35 - 35) = -61.5 [cm-1] --> A I+R
freq ( 36 - 36) = -51.6 [cm-1] --> A I+R
freq ( 37 - 37) = -50.5 [cm-1] --> A I+R
freq ( 38 - 38) = -48.8 [cm-1] --> A I+R
freq ( 39 - 39) = -42.3 [cm-1] --> A I+R
freq ( 40 - 40) = -35.4 [cm-1] --> A I+R
freq ( 41 - 41) = -35.0 [cm-1] --> A I+R
freq ( 42 - 42) = -31.2 [cm-1] --> A I+R
freq ( 43 - 43) = -27.1 [cm-1] --> A I+R
freq ( 44 - 44) = -24.7 [cm-1] --> A I+R
freq ( 45 - 45) = -22.7 [cm-1] --> A I+R
freq ( 46 - 46) = -17.6 [cm-1] --> A I+R
freq ( 47 - 47) = -15.2 [cm-1] --> A I+R
freq ( 48 - 48) = -13.7 [cm-1] --> A I+R
freq ( 49 - 49) = -10.4 [cm-1] --> A I+R
freq ( 50 - 50) = -9.7 [cm-1] --> A I+R
freq ( 51 - 51) = -6.7 [cm-1] --> A I+R
freq ( 52 - 52) = -5.3 [cm-1] --> A I+R
freq ( 53 - 53) = -4.6 [cm-1] --> A I+R
freq ( 54 - 54) = -3.5 [cm-1] --> A I+R
freq ( 55 - 55) = -2.2 [cm-1] --> A I+R
freq ( 56 - 56) = -1.8 [cm-1] --> A I+R
freq ( 57 - 57) = -0.8 [cm-1] --> A I+R
freq (133 -133) = 41.4 [cm-1] --> A I+R
freq (134 -134) = 90.8 [cm-1] --> A I+R
freq (135 -135) = 100.3 [cm-1] --> A I+R
freq (136 -136) = 118.5 [cm-1] --> A I+R
freq (137 -137) = 225.3 [cm-1] --> A I+R
freq (138 -138) = 265.3 [cm-1] --> A I+R
freq (139 -139) = 299.9 [cm-1] --> A I+R
freq (140 -140) = 337.8 [cm-1] --> A I+R
freq (141 -141) = 345.5 [cm-1] --> A I+R
freq (142 -142) = 363.2 [cm-1] --> A I+R
freq (143 -143) = 366.9 [cm-1] --> A I+R
freq (144 -144) = 374.8 [cm-1] --> A I+R
freq (145 -145) = 409.4 [cm-1] --> A I+R
freq (146 -146) = 450.7 [cm-1] --> A I+R
freq (147 -147) = 473.6 [cm-1] --> A I+R
freq (148 -148) = 510.7 [cm-1] --> A I+R
freq (149 -149) = 531.8 [cm-1] --> A I+R
freq (150 -150) = 587.4 [cm-1] --> A I+R
freq (151 -151) = 598.4 [cm-1] --> A I+R
freq (152 -152) = 649.9 [cm-1] --> A I+R
freq (153 -153) = 661.2 [cm-1] --> A I+R
freq (154 -154) = 675.6 [cm-1] --> A I+R
freq (155 -155) = 679.4 [cm-1] --> A I+R
freq (156 -156) = 710.6 [cm-1] --> A I+R
freq (157 -157) = 723.0 [cm-1] --> A I+R
freq (158 -158) = 732.6 [cm-1] --> A I+R
freq (159 -159) = 739.0 [cm-1] --> A I+R
freq (160 -160) = 740.3 [cm-1] --> A I+R
freq (161 -161) = 759.1 [cm-1] --> A I+R
freq (162 -162) = 760.7 [cm-1] --> A I+R
freq (163 -163) = 802.2 [cm-1] --> A I+R
freq (164 -164) = 803.1 [cm-1] --> A I+R
freq (165 -165) = 833.7 [cm-1] --> A I+R
freq (166 -166) = 848.8 [cm-1] --> A I+R
freq (167 -167) = 939.7 [cm-1] --> A I+R
freq (168 -168) = 943.3 [cm-1] --> A I+R
freq (169 -169) = 959.1 [cm-1] --> A I+R
freq (170 -170) = 1061.8 [cm-1] --> A I+R
freq (171 -171) = 1130.3 [cm-1] --> A I+R
freq (172 -172) = 1140.0 [cm-1] --> A I+R
freq (173 -173) = 1200.9 [cm-1] --> A I+R
freq (174 -174) = 1235.2 [cm-1] --> A I+R
freq (175 -175) = 1238.0 [cm-1] --> A I+R
freq (176 -176) = 1249.0 [cm-1] --> A I+R
freq (177 -177) = 1276.7 [cm-1] --> A I+R
freq (178 -178) = 1290.4 [cm-1] --> A I+R
freq (179 -179) = 1335.6 [cm-1] --> A I+R
freq (180 -180) = 1358.4 [cm-1] --> A I+R
freq (181 -181) = 1370.6 [cm-1] --> A I+R
freq (182 -182) = 1372.7 [cm-1] --> A I+R
freq (183 -183) = 1391.0 [cm-1] --> A I+R
freq (184 -184) = 1406.3 [cm-1] --> A I+R
freq (185 -185) = 1420.2 [cm-1] --> A I+R
freq (186 -186) = 1434.5 [cm-1] --> A I+R
freq (187 -187) = 1454.8 [cm-1] --> A I+R
freq (188 -188) = 1465.7 [cm-1] --> A I+R
freq (189 -189) = 1472.9 [cm-1] --> A I+R
Best Regards
Elham
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20150716/c96fe825/attachment.html>
More information about the users
mailing list