From e057388b7db36ec246e1efa27823d166aa0b47db Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 8 Feb 2008 21:01:37 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1480 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Eqs/Script.create | 1 + doc/Eqs/pair_cmm.jpg | Bin 0 -> 7229 bytes doc/Eqs/pair_cmm.tex | 16 ++++ doc/Section_commands.html | 10 ++- doc/Section_commands.txt | 8 ++ doc/angle_cmm.html | 65 ++++++++++++++ doc/angle_cmm.txt | 60 +++++++++++++ doc/pair_cmm.html | 176 ++++++++++++++++++++++++++++++++++++++ doc/pair_cmm.txt | 167 ++++++++++++++++++++++++++++++++++++ 9 files changed, 502 insertions(+), 1 deletion(-) create mode 100644 doc/Eqs/pair_cmm.jpg create mode 100644 doc/Eqs/pair_cmm.tex create mode 100644 doc/angle_cmm.html create mode 100644 doc/angle_cmm.txt create mode 100644 doc/pair_cmm.html create mode 100644 doc/pair_cmm.txt diff --git a/doc/Eqs/Script.create b/doc/Eqs/Script.create index ee5eadd65f..3512fabb23 100755 --- a/doc/Eqs/Script.create +++ b/doc/Eqs/Script.create @@ -31,6 +31,7 @@ latex pair_airebo latex pair_buck latex pair_charmm latex pair_class2 +latex pair_cmm latex pair_colloid_cc latex pair_colloid_cs latex pair_colloid_ss diff --git a/doc/Eqs/pair_cmm.jpg b/doc/Eqs/pair_cmm.jpg new file mode 100644 index 0000000000000000000000000000000000000000..f97a47393b45e5f1bd973f9a27cc4026ef243766 GIT binary patch literal 7229 zcmZ8m2T)U8x4oeS0jW|2f)eDTDph)i1dv{(N>@NYdIt-jlmG#O2!t-uds7jV5~?UI zKmbvKkrH}9`t$RD@6Eio&&-~=bLX6W?%XwNt+UU?%*7JGsHdZ=1Assv0RCqH7dSu@ zpd_cDpdhFGlPD=Eslas9;6K4YOM8iqiGi7!iGhiUg^in?CJ5HvYOh?{(;4fpP*7^ zE=2-@(g9DNA~PB;<^bw{3#bC;!~GJ;E*$-l!`HQ0hD9oM67S}ug47P7XH;4f4@ruZ z@r$_+^xdpgols?QS>%2UJVS8869&l3!S=rs2iOn8J=xdSw;qy6K6m-7>SQu?1)$qx z6-sS_nABRM|E&JEghcX6@MyS&TZ^Y_JauN%J2Y8x(F_T5$7@}B`hfYGzG_^kw(cv} z?53`kVrsj{yxUMeb#MWHZq$v>D1w=-S8Y~Vxu*nFQrbIi@`QI9h>elRds}e&YA&W@ z^a8ksxf7FN({(5pgXg3zIXDdYiko}6lxiZ{`L^+Wj^K+hs$iv^Il>U2>Jl&b^SiGA zz4Id$;Q{l5rkj4?UvRv?s<@8n{=w&If>m%!Dc4zxJXcw7%DZWy2u+b9)#mD2#QUS~ zv3!hbgQtS_Y4h!L$aR;mCW*F810$$fs@%!!0Z8>db)V>Hx~NlLU_aR{#)Me)s~OeW zYO2djapateILb?_;388K->@(bz}Isg7Asm#T0WecG)NK*T(x>Pu3@BHX}ufDO~1vR zW<-vrP^q26eO=G?L_rfVL&e=p{J2d+z6s)5 z%$i!)ezrz){7dFw%d6@|Rexf<#GdNqxllpWaskN*{MpW~MTz-YlC95p7U9E<=b)p= z&kU-=>jkW}v#211fx+Bb*iT(v<`N9HW$*%+xUno0PIy@JbsvTCYP-Uf$GAHfK4PrS z&&9Z5Grs#)jSdaNiCxFTU=53+_re&X*(m~>?@#-OZ& z@PiYMmwloUbL-7aW;NW5xDH88*1%13ZpF03dEUv*qllrsWhn?vcv5ls8c$~U1@N5f zET5QPa;#_>-n5_Gpq5t7cP;1K*#)VI8>3k~r@wzM=2N753r+OrVf8Dug`t-nLL9ah zwPRKN8R|#l&4>zBuVt*b&=YU=_r2dx7Bz*-&6DGqtGfvXswRQwKRptRI;S?=QX=w& zaR^Hb0s?Lt$_c}ct&?C{p1J31Q9Uy`aJ)i~Wf)`h&dt*0v*fzpU6WU&10H1iPQE1? zzID%kT_?UG(<&~hqsS`ofbp5-J;&y~L8Bm1x`Jm`$39yy&DYaGsCQKx6E(~a1rr_} zYvu6B3FPFz6k&}fkBE&?%Gmbt$o`H(3h|VN`^hj9H!pyM;Dq*bj|svNe(ZV77uK$1 z&kLaI<15iWkduP6t&6mToLm;8&ueOIv$DfcFC+X?gheC|w!4Fy-m)4&Z&M&k1}BKJ zSAuMg4irWFCMw86hNVBVGDZ!`8|Fs!&sy!X)l_0#E&$9!{`(1#z^A>*Q5c5RsE@ui zQ-fu71}kub7iu6Ab)Jz(5NXLjvY>Epe}te#a;q(`tLtP-yf1^T9F?>sO?{E}Nn}TW zzMssdx9{>hYwUuiTsSj}#!rOvz22^6&6}h8KX-aoB2An{dcbcit{it+X3d=V8?9t3 zE7!GYRAXEs9Xp-fQ4gjex=Oz-wD1R&Z!E}>MifY0L8u+}qo)b9(bkd{*K4_w9OGQi zeIB-Bd)Mauy0pK&yF)0meGV3vDmI{<;0mew5M}j z7+e5^q#r^dZMikI&t}#k7rHo&1Qt&FF)pvRk#q^yb zjd!^f6D8yC$>9%pjUabE2e~&+6P8lW9#VJOHvNKELB9TE+~ZJ9zt>S{Scn}Qe-xy2 zL$_soLjTPG=*A7>kDb4ln|C93`lA9rFKx*r#q2xu*ddtG#f8B^_rLbg_d8+6<|6mz zt5srO=?VSbN;*+|(4$>Bp>Fg(=EtbW(65+V>D}Mns=qpQk+=XDv$t`Z$qTp63=FVE zPGcnI(Xc|JpYEaT7r>j9G1IN3uQU!VBB(`TX%&r?IrJSPSb3x*R^Ej$YkekZy7AqB zaoz!8A4qGpBUP40j&)f4$uI|}geh&qwY5&W2W?s?~6KkDg#w`^$3Op{~SL6(3>;p1dK*xwxH{V5! zIFH5G^hwG3@0kd7h;RSzvm>@|<(gJ|RZKv!xcI1wE>{7rcLqW`IV_Z@Fs&D+4H3hxqU@@O?%|FhDtqvyEC*Iga@cnXCph?{g_PGitBxnb_V4E;F3pth~8ytRS0 zWlnG1L0ziuUbJEYupLI^-essCJhGp>0PxcjXP31;ENb>Yw5-j<2iY`;Nc(V5 zQGZ~7ILdP++?lScp1WV}+EDZsYP~8Md@OV`q>AxgWWPRh$wy$Z7+>XfZhz#);my+1wnsS{o ztvtA9%lwcOcU_#ko_z`bcryy|VCR3e?6074P?=VPDE!oqSHu%MN-~@ROy1Op8d>VF z9C(!_((lYsGiNe2g*k#=ocHuiOXQ7g(_XK5rD|7{raiAX^aSLi{2TvxjF7kLSQ0oS zG+*cXX#x4X%xc3&erY?BSLKMGqhC_y?Ihh3V!H_YuCr1npM-Y z6_?wZRoQkhbPW@);QH|IjM8t)*irYuk9e2G9{u-LIcZ(mCf8pl^2Cp4$-66QWz1O5 zUI4QcM+Yi1C9PAA4FaBu3YO(BGQdai zZk2#IO02lXjsy!Lz=HED9{MDTi1w|v;&d_n*RMv9$7wUyn3A+k>9=V!Rg{!`K7PF6#o~vOGlg2#{nuS;5A3!-aqT2g@9eJFAz}OtFvNC1_NP@@7EHTWr*8XV zH9MvC&vs!BU2{v1$LrXH&ajMzB=Vl#A-ScDrjaep3!q#z+4|os?Cnc@J3Sh1silx2 z$B6q5^0Le)506aWt-e3dTZi%>PoMetT6aoWikBGZAH-H9TfI=FUE41xh|Gg% zy0RA=bJc-#y!A^VKRLk$Bi`t|h~J+fm+2zti)MVNvV$sxbUu9OjF`kfcCKN8y8vA| zJnv>2cG=?`-^pG8oSM@(+wf!73eP)^uVqn`dc1E0n1)bc)=`#nQ{Pf~`ZRWF=`tGU zJr%snC>FFQuT=CuXR6r{)wa_cdXIu0)CoR;0}L^Mt9S`+#t@xa5gxu06{k=*gZ@Wv zs7>UJN?}U&=@O8&v<)XJ1h$K}KOj0vaB{X7-*&n4h|0s=vzsSG-9 z^tqAc+ho9SD`kye(b4l1zPyWJV~OJrZGzYym?CZ}kMgtz^Qy%5%kLfG=gZgiFWHvW z4GW}XIjtVN2%21JaiV1`tTwKKFTx4U{$Rm$4F7POEj_xkbdB=T6d|Cg`5jGbOm|eH zw&A=NOv_XrF=z7ROMBsG9EZ6X0;8=% zJsDfW_PLM8CWQ~)oMyTkm4)z#m2?>T=ledqukK9q_*l@JBYf|Y8&c;~{w6=GgYC+B z!}3r0>b3Gy)!xmd`n*}vK@0I?sssizhbvT{RF{@2Frl&b$^MW^93EYH z7`@FJdjWW_sP<8gr|c)y=T>BGu6}cr!|oG_PsAQTf2wn*X$@XUnbQmyT+#{UCJXMA zcw6)ydsSf$C%mmKSTY-7<(%{cP~k^QJHKbz17X?;X`#ixMK6Gph6yX~15@4mn6Yzi z=J!Gu0G*5AspffX&8dsk**V?Ue^JKLye3}ZQ!}@JkYQi*s?Q$Y#qi^9CY1+D&SX}X zTkoqp7~@$1mDrZaP1^P(1q!PQQ#ll7i|&pERk4wy18?yPPwGpown zZGwqfZVZ6G1f$}m22{eb)A!AYCGFm2w@-y%c>A#`o^_}w=Hj{!`NEcXm44cO#~KGQ zn0W@C;G|o2JcFfO>+7z{WuSkZQPG6)G+s;pO<4I37Mq99xNzo`j~h>{8MGN&;Wm&5 zQ%?Gqd!ZE1Zl$olJOwQh4jbe>3a4%q=XQ(X-ibCTP26q%SoX)!p}$-KMN)s;u&O7es|qVNK<%kZl}AlCmr(yjJvUX%{L3D z?+0tJf56xvJ440?_}lHOEzw8r$_+6jSeC!VtLZl}_k2+2 zr*PJ*;GI9H**r8e3s5s_Tcf;Ng1(*d&OzSA@7G%N_e_Y=(+zcs1z_8&j7-VyOVPTt2P>PN z>2Sep=qrjE$9M|VZ9pQi%N!#KCPLU#!_}yFfC#QCz=S{MXIGh$Rzcy9=HY$(063$2 zSfzT=X5vFFS2(^?rGL#l#U=($rtYr7`hu7Ojq!Drzp*&ud2D0b$rr9hA z?k@~%E31Fh4dn&Wtr^O}pN(eC5a+d@KRghy-ss+b*S}CpE=2KkU&X&9Xd>R>nNRk( zU4~`)6r!40r&m%dzoh=w?)&1bONC9Q%9!m3jYnmMwG0$qt9BGApKy+QML%*(S9L^}unIVU@w%$~BqHmM>B{T*CFD zaO>DVBuXC&1RT-jCJ*gv&nm}*j(zbZu7pOfY8kC3|uUrOblSs9soe)Y|@g+9?Q zcdcU>ZY3jdOku*c)O&LyBc*<@0QyjOszAmbvMW#i`Ju6~VxmTwlO(Z2f+CG3k^WQ( z29Bm;1ISVLQQT$csTa?0^78_`0LVh4I97?0dpGRHFh{?}!n&}JOn_Hy)yp!X@<5-% zZA&^twNjM`rJEC;kzqoi&mxMe$}O&=3a|__i8wjY%iabo`Rcd9@%*^!TY*!DH}XOR za<`|d#S&^uDe^Ohz&nE$K9E?LfE60XH|uWogJYg7$vT^ee;S#8 z+zqmLLHH$Q@qgW%$^Q8_kLJ0Jk_=nZ%R!3FmWZJCF=<5Shn?el|LjH{7C0@BC5^cJ zQ@S>)6?|w>D$CUT6(-jBB~31)tF5g->;yd4)`pfe%m}ga@^CVgE3fmlm+bMp6uYT0 zP+OiQ02dxor#RUT<$L_#53Fdtn(At0T(Vq|5dq;cMalF>b|UiRNZ`9kE>dmhaEYsC z%-CCKYTCQX(>dGL-!om$drTnWRxS(F>o|jH_d_96N{E~3?@9Ns7nLjznzTt#>2a)^ zu|_G{a&jp=5_kZWk}OdaJ`mbvy_<@^^tm}CeEpq#P+DhP+Z7Qhn9N;gF%AqHNk(B}|QNE`A@Ms~U!J?v%86*iHo>yOTN|!lc1Y)hL&dc=7Ef4I@&gZ0LXs zq16?PEK3fRUQjoxI4%h@2zq#9sFcZ6*CQhi$;4+Sc^%GF2p`dNg9!aX`vOPCQy*4N*q$vY5KExFNf zLbkC{h||O)-(w%!f)|yqCt1;gNjsIG&Bx1r)LYzf&LB&oFMrnklN!se>cUlYX|b@k z$aDIn-c%D zf3h!?DSUGJM$U}S@CSh3IdSU>NEN)AbOFRQHk`kjGFbub69vU13;0P%%STZRd4!tT z=<6Ggq6@}xn*@@~@(-PDqtxlPtpgP*yJbFK;+T=$m?ft`{)|rCwFhJ@XTcWSX(bsL zEJB`}fLyyhIv#X>jUJ7)?x@eL5;8C2c?mV%n<=VEoy@FvTvvq8rx|4oY=V`2b+TC; ziub3>^3c{Z)>#RgOs9oW?=uL4^6JG60tUA&Y?D$=dEy3H(g#+|nJ$1mxj=2<3*d*M zZe3L5i7?^y(u)er^%tTQ)rI|>v#@{&|B;f6LH=(d#~O2{)VeVA);`ZsQmPBD;*A+?i7`&S0RC}N9sXmi6yJ^J zv8}|5BNlD7oZ0Tbe$A|Y2-*;NbkZ$<+aP*jKfUIGELZU}N?TuY_ESt5e=4MaGyiSB zV@h~tjOUqRP{|$%IcnT{0UTpf+XT1LqOY5<_$*`;9Tx<*l0KCUl7jEUu6*I7<=Xn4 z#MJc-8S4*SZa)!kdVLTQ-0aY|iJtxCc2|$)5MR4{Yl(OJ9!i_2l)mzK#RwsHBVnlt zvg1{qFe{>**gzjulGvMGc&?Wy8Plu!i{@LuOw6~XQMNzC!1<&rqDodd==~~D_D73^ zl_3fRt8FZ08QK#FQt5rV%I+7Y6dWfq_Gorf%m`-Xyx_?u%c9NcS_4vtmT%Cey+7Z} ziQ=h>vab0(I{uZ3(PPS3Qqx%_>e)EF;uaVI^VEuwX)DJlV}mZ3I-GbS6GPt z6#vo9lfBB;+I4^BmR>E>iDodG;pyB^sHz477P>6Nw`wnX)fNZ8-o`q-a=F6vbZK}- z&LK2f4oCyGepKV9}A!_$CSHpC;LjWsZIm^>H3$>RF0n zy!VD!)#Ht!AG+C1t&XA*cHxhUY5k+oIL`-c46uF`T8lyhs1M1*8vz?Hvzv%ERX23|NJI zZ)IJ9-0Z^$TQPP0+E$8PgCakL z#k&dIcy>0feJ$-w-c%`ckloYjokloY3CYWdMN^nfRr1ynBI@*MR=)N`;B94r+jr1w z&8~6RERwp-HK;XI-e|;$kW67%(Knh(Lf4v<0`&P0B@j0aV6k%K$Y?Y^i#zv4@VfDB2t5-WW(2lxXmV*{x%5vlAjXuzG4>fNpd2!)8q@8j6%@ zrZ&BEpuoVQJL4Ig3p-Ei;KWYtqbcRUX5UX&b*{nfMX^dg3xtuRrwk U^S=)Czi&_e^NIie@nZJB01wRLAMMPS is built with the appropriate package.

@@ -396,6 +397,13 @@ itself for a full description: cosinecosine/deltacosine/squaredharmonic +

These are angle styles contributed by users, which can be used if +LAMMPS is built with the appropriate package. +

+
+
cg/cmm +
+

Dihedral_style potentials. See the diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index b7b4f7fb87..468ef02a66 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -521,6 +521,9 @@ These are pair styles contributed by users, which can be used if "LAMMPS is built with the appropriate package"_Section_start.html#2_3. "buck/coul"_pair_buck_coul.html, +"cg/cmm"_pair_cmm.html, +"cg/cmm/coul/cut"_pair_cmm.html, +"cg/cmm/coul/long"_pair_cmm.html, "lj/coul"_pair_lj_coul.html :tb(c=4,ea=c) :line @@ -554,6 +557,11 @@ itself for a full description: "cosine/squared"_angle_cosine_squared.html, "harmonic"_angle_harmonic.html :tb(c=4,ea=c,w=100) +These are angle styles contributed by users, which can be used if +"LAMMPS is built with the appropriate package"_Section_start.html#2_3. + +"cg/cmm"_angle_cmm.html :tb(c=4,ea=c) + :line Dihedral_style potentials. See the diff --git a/doc/angle_cmm.html b/doc/angle_cmm.html new file mode 100644 index 0000000000..d994d98a6d --- /dev/null +++ b/doc/angle_cmm.html @@ -0,0 +1,65 @@ + +

LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
+ + + + + + +
+ +

angle_style cg/cmm command +

+

Syntax: +

+
angle_style cg/cmm 
+
+

Examples: +

+
angle_style cg/cmm
+angle_coeff 1 300.0 107.0 lj9_6 0.4491 3.7130 
+
+

Description: +

+

The cg/cmm angle style is a combination of the harmonic angle potential, +

+
+
+

where theta0 is the equilibrium value of the angle and K a prefactor, +with the repulsive part of the non-bonded cg/cmm pair style +between the atoms 1 and 3. This angle potential is intended for +coarse grained MD simulations with the CMM parametrization using the +pair_style cg/cmm. Relative to the pair_style +cg/cmm, however, the energy is shifted by epsilon, to avoid sudden +jumps. Note that the usual 1/2 factor is included in K. +

+

The following coefficients must be defined for each angle type via the +angle_coeff command as in the example above. As +with other CMM coarse grained parameters, they cannot be set in the +data file, but can be restored from restarts via the +read_restart command: +

+
  • K (energy/radian^2) +
  • theta0 (degrees) +
  • cg_type (string, one of lj9_6, lj12_4, lj12_6) +
  • epsilon (energy units) +
  • sigma (distance units) +
+

Theta0 is specified in degrees, but LAMMPS converts it to radians +internally; hence the units of K are in energy/radian^2. +

+

Restrictions: +

+

This angle style can only be used if LAMMPS was built with the +"user-cg-cmm" package. See the Making LAMMPS section +for more info on packages. +

+

Related commands: +

+

angle_coeff, angle_style +harmonic, pair_style cg/cmm +

+

Default: none +

+ diff --git a/doc/angle_cmm.txt b/doc/angle_cmm.txt new file mode 100644 index 0000000000..69eaa1dbe7 --- /dev/null +++ b/doc/angle_cmm.txt @@ -0,0 +1,60 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +angle_style cg/cmm command :h3 + +[Syntax:] + +angle_style cg/cmm :pre + +[Examples:] + +angle_style cg/cmm +angle_coeff 1 300.0 107.0 lj9_6 0.4491 3.7130 :pre + +[Description:] + +The {cg/cmm} angle style is a combination of the harmonic angle potential, + +:c,image(Eqs/angle_harmonic.jpg) + +where theta0 is the equilibrium value of the angle and K a prefactor, +with the {repulsive} part of the non-bonded {cg/cmm} pair style +between the atoms 1 and 3. This angle potential is intended for +coarse grained MD simulations with the CMM parametrization using the +"pair_style cg/cmm"_pair_cmm.html. Relative to the pair_style +{cg/cmm}, however, the energy is shifted by {epsilon}, to avoid sudden +jumps. Note that the usual 1/2 factor is included in K. + +The following coefficients must be defined for each angle type via the +"angle_coeff"_angle_coeff.html command as in the example above. As +with other CMM coarse grained parameters, they cannot be set in the +data file, but can be restored from restarts via the +"read_restart"_read_restart.html command: + +K (energy/radian^2) +theta0 (degrees) +cg_type (string, one of lj9_6, lj12_4, lj12_6) +epsilon (energy units) +sigma (distance units) :ul + +Theta0 is specified in degrees, but LAMMPS converts it to radians +internally; hence the units of K are in energy/radian^2. + +[Restrictions:] + +This angle style can only be used if LAMMPS was built with the +"user-cg-cmm" package. See the "Making LAMMPS"_Section_start.html#2_3 section +for more info on packages. + +[Related commands:] + +"angle_coeff"_angle_coeff.html, "angle_style +harmonic"_angle_harmonic.html, "pair_style cg/cmm"_pair_cmm.html + +[Default:] none diff --git a/doc/pair_cmm.html b/doc/pair_cmm.html new file mode 100644 index 0000000000..239c495a26 --- /dev/null +++ b/doc/pair_cmm.html @@ -0,0 +1,176 @@ + +
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
+ + + + + + +
+ +

pair_style cg/cmm command +

+

pair_style cg/cmm/coul/cut command +

+

pair_style cg/cmm/coul/long command +

+

Syntax: +

+
pair_style style args 
+
+
  • style = cg/cmm or cg/cmm/coul/cut or cg/cmm/coul/long +
  • args = list of arguments for a particular style +
+
  cg/cmm args = cutoff
+    cutoff = global cutoff for Lennard Jones interactions (distance units)
+  cg/cmm/coul/cut args = cutoff (cutoff2) (kappa)
+    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+    cutoff2 = global cutoff for Coulombic (optional) (distance units)
+    kappa = Debye length (optional, defaults to 0.0 = disabled) (inverse distance units)
+  cg/cmm/coul/long args = cutoff (cutoff2)
+    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+    cutoff2 = global cutoff for Coulombic (optional) (distance units) 
+
+

Examples: +

+
pair_style cg/cmm 2.5
+pair_coeff 1 1 lj12_6 1 1.1 2.8 
+
+
pair_style cg/cmm/coul/cut 10.0 12.0
+pair_coeff 1 1 lj9_6  100.0 3.5 9.0
+pair_coeff 1 1 lj12_4 100.0 3.5 9.0 9.0 
+
+
pair_style cg/cmm/coul/long 10.0
+pair_style cg/cmm/coul/long 10.0 8.0
+pair_coeff 1 1 lj9_6 100.0 3.5 9.0 
+
+

Description: +

+

The cg/cmm styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential, +given by +

+
+
+

as required for the CMM Coarse-grained MD parametrization discussed in +(Shinoda). Rc is the cutoff. +

+

Style cg/cmm/coul/cut adds a Coulombic pairwise interaction given by +

+
+
+

where C is an energy-conversion constant, Qi and Qj are the charges on +the 2 atoms, and epsilon is the dielectric constant which can be set +by the dielectric command. If one cutoff is +specified in the pair_style command, it is used for both the LJ and +Coulombic terms. If two cutoffs are specified, they are used as +cutoffs for the LJ and Coulombic terms respectively. +

+

This style also contains an additional exp() damping factor +to the Coulombic term, given by +

+
+
+

where kappa is the Debye length (kappa=0.0 is the unscreened coulomb). +This potential is another way to mimic the screening effect of a polar +solvent. +

+

Style cg/cmm/coul/long computes the same Coulombic interactions as +style cg/cmm/coul/cut except that an additional damping factor is +applied to the Coulombic term so it can be used in conjunction with +the kspace_style command and its ewald or pppm +option. The Coulombic cutoff specified for this style means that +pairwise interactions within this distance are computed directly; +interactions outside that distance are computed in reciprocal space. +

+

The following coefficients must be defined for each pair of atoms +types via the pair_coeff command as in the examples +above, or in the data file or restart files read by the +read_data or read_restart +commands, or by mixing as described below: +

+
  • cg_type (lj9_6, lj12_4, or lj12_6) +
  • epsilon (energy units) +
  • sigma (distance units) +
  • cutoff1 (distance units) +
  • cutoff2 (distance units) +
+

Note that sigma is defined in the LJ formula as the zero-crossing +distance for the potential, not as the energy minimum. The prefactors +are chosen so that the potential minimum is at -epsilon. +

+

The latter 2 coefficients are optional. If not specified, the global +LJ and Coulombic cutoffs specified in the pair_style command are used. +If only one cutoff is specified, it is used as the cutoff for both LJ +and Coulombic interactions for this type pair. If both coefficients +are specified, they are used as the LJ and Coulombic cutoffs for this +type pair. +

+

For cg/cmm/coul/long only the LJ cutoff can be specified since a +Coulombic cutoff cannot be specified for an individual I,J type pair. +All type pairs use the same global Coulombic cutoff specified in the +pair_style command. +

+
+ +

Mixing, shift, table, tail correction, per-atom energy/stress, +restart, and rRESPA info: +

+

For atom type pairs I,J and I != J, the epsilon and sigma coefficients +and cutoff distance for all of the cg/cmm pair styles cannot be mixed, +since different pairs may have different exponents. So all parameters +for all pairs have to be specified explicitly through the "pair_coeff" +command. Defining then in a data file is also not supported, due to +limitations of that file format. +

+

All of the cg/cmm pair styles support the +pair_modify shift option for the energy of the +Lennard-Jones portion of the pair interaction. +

+

The cg/cmm/coul/long pair styles support the +pair_modify table option since they can tabulate +the short-range portion of the long-range Coulombic interaction. +

+

All of the cg/cmm pair styles can calculate per-atom energy and +stress, as used by the compute epair/atom, +compute stress/atom, and dump +custom commands. +

+

All of the cg/cmm pair styles write their information to binary +restart files, so pair_style and pair_coeff commands do +not need to be specified in an input script that reads a restart file. +

+

The cg/cmm, cg/cmm/coul/cut and lj/cut/coul/long pair styles support +the use of the inner, middle, and outer keywords of the run_style +respa command, meaning the pairwise forces can be +partitioned by distance at different levels of the rRESPA hierarchy. +See the run_style command for details. +

+
+ +

Restrictions: +

+

All of the cg/cmm pair styles are part of the "user-cg-cmm" +package. They are only enabled if LAMMPS was built with that +package. The cg/cmm/coul/long style also requires the "kspace" +package to be built (which is enabled by default). See the Making +LAMMPS section for more info. +

+

On some 64-bit machines, compiling with -O3 appears to break the +Coulombic tabling option used by the cg/cmm/coul/long style. See +the "Additional build tips" section of the Making LAMMPS documentation +pages for workarounds on this issue. +

+

Related commands: +

+

pair_coeff, angle_style cg/cmm +

+

Default: none +

+
+ + + +

(Shinoda) Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007). +

+ diff --git a/doc/pair_cmm.txt b/doc/pair_cmm.txt new file mode 100644 index 0000000000..495e652707 --- /dev/null +++ b/doc/pair_cmm.txt @@ -0,0 +1,167 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style cg/cmm command :h3 +pair_style cg/cmm/coul/cut command :h3 +pair_style cg/cmm/coul/long command :h3 + +[Syntax:] + +pair_style style args :pre + +style = {cg/cmm} or {cg/cmm/coul/cut} or {cg/cmm/coul/long} +args = list of arguments for a particular style :ul + {cg/cmm} args = cutoff + cutoff = global cutoff for Lennard Jones interactions (distance units) + {cg/cmm/coul/cut} args = cutoff (cutoff2) (kappa) + cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) + kappa = Debye length (optional, defaults to 0.0 = disabled) (inverse distance units) + {cg/cmm/coul/long} args = cutoff (cutoff2) + cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre + +[Examples:] + +pair_style cg/cmm 2.5 +pair_coeff 1 1 lj12_6 1 1.1 2.8 :pre + +pair_style cg/cmm/coul/cut 10.0 12.0 +pair_coeff 1 1 lj9_6 100.0 3.5 9.0 +pair_coeff 1 1 lj12_4 100.0 3.5 9.0 9.0 :pre + +pair_style cg/cmm/coul/long 10.0 +pair_style cg/cmm/coul/long 10.0 8.0 +pair_coeff 1 1 lj9_6 100.0 3.5 9.0 :pre + +[Description:] + +The {cg/cmm} styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential, +given by + +:c,image(Eqs/pair_cmm.jpg) + +as required for the CMM Coarse-grained MD parametrization discussed in +"(Shinoda)"_#Shinoda. Rc is the cutoff. + +Style {cg/cmm/coul/cut} adds a Coulombic pairwise interaction given by + +:c,image(Eqs/pair_coulomb.jpg) + +where C is an energy-conversion constant, Qi and Qj are the charges on +the 2 atoms, and epsilon is the dielectric constant which can be set +by the "dielectric"_dielectric.html command. If one cutoff is +specified in the pair_style command, it is used for both the LJ and +Coulombic terms. If two cutoffs are specified, they are used as +cutoffs for the LJ and Coulombic terms respectively. + +This style also contains an additional exp() damping factor +to the Coulombic term, given by + +:c,image(Eqs/pair_debye.jpg) + +where kappa is the Debye length (kappa=0.0 is the unscreened coulomb). +This potential is another way to mimic the screening effect of a polar +solvent. + +Style {cg/cmm/coul/long} computes the same Coulombic interactions as +style {cg/cmm/coul/cut} except that an additional damping factor is +applied to the Coulombic term so it can be used in conjunction with +the "kspace_style"_kspace_style.html command and its {ewald} or {pppm} +option. The Coulombic cutoff specified for this style means that +pairwise interactions within this distance are computed directly; +interactions outside that distance are computed in reciprocal space. + +The following coefficients must be defined for each pair of atoms +types via the "pair_coeff"_pair_coeff.html command as in the examples +above, or in the data file or restart files read by the +"read_data"_read_data.html or "read_restart"_read_restart.html +commands, or by mixing as described below: + +cg_type (lj9_6, lj12_4, or lj12_6) +epsilon (energy units) +sigma (distance units) +cutoff1 (distance units) +cutoff2 (distance units) :ul + +Note that sigma is defined in the LJ formula as the zero-crossing +distance for the potential, not as the energy minimum. The prefactors +are chosen so that the potential minimum is at -epsilon. + +The latter 2 coefficients are optional. If not specified, the global +LJ and Coulombic cutoffs specified in the pair_style command are used. +If only one cutoff is specified, it is used as the cutoff for both LJ +and Coulombic interactions for this type pair. If both coefficients +are specified, they are used as the LJ and Coulombic cutoffs for this +type pair. + +For {cg/cmm/coul/long} only the LJ cutoff can be specified since a +Coulombic cutoff cannot be specified for an individual I,J type pair. +All type pairs use the same global Coulombic cutoff specified in the +pair_style command. + +:line + +[Mixing, shift, table, tail correction, per-atom energy/stress, +restart, and rRESPA info]: + +For atom type pairs I,J and I != J, the epsilon and sigma coefficients +and cutoff distance for all of the cg/cmm pair styles {cannot} be mixed, +since different pairs may have different exponents. So all parameters +for all pairs have to be specified explicitly through the "pair_coeff" +command. Defining then in a data file is also not supported, due to +limitations of that file format. + +All of the cg/cmm pair styles support the +"pair_modify"_pair_modify.html shift option for the energy of the +Lennard-Jones portion of the pair interaction. + +The {cg/cmm/coul/long} pair styles support the +"pair_modify"_pair_modify.html table option since they can tabulate +the short-range portion of the long-range Coulombic interaction. + +All of the cg/cmm pair styles can calculate per-atom energy and +stress, as used by the "compute epair/atom"_compute_epair_atom.html, +"compute stress/atom"_compute_stress_atom.html, and "dump +custom"_dump.html commands. + +All of the cg/cmm pair styles write their information to "binary +restart files"_restart.html, so pair_style and pair_coeff commands do +not need to be specified in an input script that reads a restart file. + +The cg/cmm, cg/cmm/coul/cut and lj/cut/coul/long pair styles support +the use of the {inner}, {middle}, and {outer} keywords of the "run_style +respa"_run_style.html command, meaning the pairwise forces can be +partitioned by distance at different levels of the rRESPA hierarchy. +See the "run_style"_run_style.html command for details. + +:line + +[Restrictions:] + +All of the cg/cmm pair styles are part of the "user-cg-cmm" +package. They are only enabled if LAMMPS was built with that +package. The {cg/cmm/coul/long} style also requires the "kspace" +package to be built (which is enabled by default). See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. + +On some 64-bit machines, compiling with -O3 appears to break the +Coulombic tabling option used by the {cg/cmm/coul/long} style. See +the "Additional build tips" section of the Making LAMMPS documentation +pages for workarounds on this issue. + +[Related commands:] + +"pair_coeff"_pair_coeff.html, "angle_style cg/cmm"_angle_cmm.html + +[Default:] none + +:line + +:link(Shinoda) +[(Shinoda)] Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).