<div dir="ltr"><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-size:10pt;font-family:'Courier New';color:black">Dear all,</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-size:10pt;font-family:'Courier New';color:black"> I want to do phonon
calculation on an adsorption system.</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt"><font color="#000000" face="Courier New"><span style="font-size:10pt">I did a test calculation on a system, an molecule is adsorbed
on a surface. I just want to calculate the </span><span style="font-size:13.3333330154419px">vibration</span><span style="font-size:10pt"> frequencies of the
molecule and </span><span style="font-size:13.3333330154419px">surrounding</span><span style="font-size:10pt"> 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!</span></font></p>
<p class="MsoNormal"><span style="font-size:10pt;line-height:107%;font-family:'Courier New';color:black">A lot of negative
frequencies because of surface atoms and molecules binding to each other this
happen?</span></p><p class="MsoNormal"><span style="font-size:10pt;line-height:107%;font-family:'Courier New';color:black"><br></span></p><p class="MsoNormal"><span style="font-size:10pt;line-height:107%;font-family:'Courier New';color:black"><br></span></p>
<p class="MsoNormal">Atomic displacements:</p>
<p class="MsoNormal"> There are 189
irreducible representations</p>
<p class="MsoNormal">
Representation 1 1 modes -A Not done in this run</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">
Representation 2 1 modes -A Not done in this run</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">
Representation 3 1 modes -A Not done in this run</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"> Representation 4
1 modes -A Not done in this run</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">
Representation 5 1 modes -A Not done in this run</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">
Representation 6 1 modes -A Not done in this run</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">
Representation 7 1 modes -A Not done in this run</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"> Representation 8
1 modes -A Not done in this run</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">
Representation 9 1 modes -A Not done in this run</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">
Representation 10 1 modes -A Not done in this run</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">
Representation 11 1 modes -A Not done in this run</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"> Representation 12
1 modes -A Not done in this run</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"> <span style="background:yellow">Representation 13
1 modes -A Done</span> (for atom
5)</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">And in the output phonon list of frequencies: \</p><p class="MsoNormal"><br></p>
<p class="MsoNormal"> freq ( 1 - 1)
= -576.0 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 2 - 2)
= -573.5 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 3 - 3)
= -570.6 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 4 - 4)
= -560.4 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 5 - 5)
= -517.5
[cm-1] --> A I+R</p>
<p class="MsoNormal"> freq ( 6 - 6)
= -515.5 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 7 - 7)
= -482.4 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 8 - 8)
= -471.4 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (
9 - 9) = -462.6
[cm-1] --> A I+R</p>
<p class="MsoNormal"> freq ( 10 - 10)
= -460.7 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 11 - 11)
= -369.1 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 12 - 12)
= -358.2 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 13 - 13)
= -332.7 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 14 - 14)
= -327.7 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 15 - 15)
= -275.8 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 16 - 16)
= -271.7
[cm-1] --> A I+R</p>
<p class="MsoNormal"> freq ( 17 - 17)
= -268.3 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 18 - 18)
= -262.7 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 19 - 19)
= -255.8 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 20 - 20) = -251.8
[cm-1] --> A I+R</p>
<p class="MsoNormal"> freq ( 21 - 21)
= -246.1 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 22 - 22)
= -234.3 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 23 - 23)
= -221.0 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 24 - 24)
= -215.0 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 25 - 25)
= -204.2 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 26 - 26)
= -195.2 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 27 - 27)
= -187.3 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 28 - 28)
= -186.7 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 29 - 29)
= -171.3 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 30 - 30)
= -146.4 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 31 - 31)
= -94.0 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 32 - 32)
= -93.1 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 33 - 33)
= -89.9 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 34 - 34) = -87.6
[cm-1] --> A I+R</p>
<p class="MsoNormal"> freq ( 35 - 35)
= -61.5 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 36 - 36)
= -51.6 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 37 - 37)
= -50.5 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 38 - 38)
= -48.8 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 39 - 39)
= -42.3 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 40 - 40)
= -35.4 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 41 - 41)
= -35.0 [cm-1] --> A I+R</p>
<p class="MsoNormal"> freq ( 42 - 42)
= -31.2 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 43 - 43)
= -27.1 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 44 - 44)
= -24.7 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 45 - 45)
= -22.7 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 46 - 46)
= -17.6 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 47 - 47)
= -15.2 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 48 - 48)
= -13.7 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 49 - 49)
= -10.4 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 50 - 50)
= -9.7 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 51 - 51)
= -6.7 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 52 - 52)
= -5.3 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 53 - 53)
= -4.6 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 54 - 54)
= -3.5 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 55 - 55)
= -2.2 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 56 - 56)
= -1.8 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq ( 57 - 57)
= -0.8 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> <span style="background-color:rgb(234,153,153)"> freq (133 -133)
= 41.4 [cm-1]
--> A I+R</span></p>
<p class="MsoNormal"> freq (134 -134)
= 90.8 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (135 -135)
= 100.3 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (136 -136)
= 118.5 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (137 -137)
= 225.3 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (138 -138) = 265.3
[cm-1] --> A I+R</p>
<p class="MsoNormal"> freq (139 -139)
= 299.9 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (140 -140)
= 337.8 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (141 -141)
= 345.5 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (142 -142)
= 363.2 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (143 -143)
= 366.9 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (144 -144)
= 374.8 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (145 -145)
= 409.4 [cm-1] --> A I+R</p>
<p class="MsoNormal"> freq (146 -146)
= 450.7 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (147 -147)
= 473.6 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (148 -148)
= 510.7 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (149 -149)
= 531.8 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (150 -150)
= 587.4 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (151 -151)
= 598.4 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (152 -152)
= 649.9 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (153 -153)
= 661.2 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (154 -154)
= 675.6 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (155 -155)
= 679.4 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (156 -156)
= 710.6 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (157 -157)
= 723.0 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (158 -158)
= 732.6 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (159 -159)
= 739.0 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (160 -160)
= 740.3 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (161 -161)
= 759.1 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (162 -162)
= 760.7 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (163 -163)
= 802.2 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (164 -164)
= 803.1 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (165 -165)
= 833.7 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (166 -166)
= 848.8 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (167 -167) = 939.7
[cm-1] --> A I+R</p>
<p class="MsoNormal"> freq (168 -168)
= 943.3 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (169 -169)
= 959.1 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (170 -170)
= 1061.8 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (171 -171)
= 1130.3 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (172 -172)
= 1140.0 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (173 -173)
= 1200.9 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (174 -174)
= 1235.2 [cm-1] --> A I+R</p>
<p class="MsoNormal"> freq (175 -175)
= 1238.0 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (176 -176)
= 1249.0 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (177 -177)
= 1276.7 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (178 -178)
= 1290.4 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (179 -179)
= 1335.6 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (180 -180)
= 1358.4 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (181 -181)
= 1370.6 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (182 -182)
= 1372.7 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (183 -183)
= 1391.0 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (184 -184)
= 1406.3 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (185 -185)
= 1420.2 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (186 -186)
= 1434.5 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (187 -187)
= 1454.8 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (188 -188)
= 1465.7 [cm-1]
--> A I+R</p>
<p class="MsoNormal"> freq (189 -189)
= 1472.9 [cm-1]
--> A I+R</p><p class="MsoNormal"><br></p><p class="MsoNormal">Best Regards</p><p class="MsoNormal">Elham</p></div>