From 25d7be5f3dd52f3e0be94ba73ffd7889dfec617b Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 17 Nov 2016 16:11:30 -0700 Subject: [PATCH] compute pressure doc change --- doc/src/Eqs/pressure.jpg | Bin 4097 -> 4333 bytes doc/src/Eqs/pressure.tex | 2 +- doc/src/Eqs/pressure_tensor.jpg | Bin 5038 -> 5457 bytes doc/src/Eqs/pressure_tensor.tex | 2 +- doc/src/Section_commands.txt | 3 ++- doc/src/compute_pressure.txt | 31 +++++++++++++++---------------- doc/src/pair_tersoff_mod.txt | 1 - doc/src/pair_vashishta.txt | 1 + src/USER-MISC/pair_agni.cpp | 2 +- 9 files changed, 21 insertions(+), 21 deletions(-) diff --git a/doc/src/Eqs/pressure.jpg b/doc/src/Eqs/pressure.jpg index 0ed67477566679e5772a36ffd71729e23477d8c3..525d8a75ee0747ad5b552a6020eddad600656ab2 100644 GIT binary patch literal 4333 zcmb_e2{@Ep`+vp^L)Jlru?`_iMA->tNw#Fko-vl!GK|R*QIb>`l(Jy{_;3uIsz6>zwCz-_P&d_kGT}pXZ!?!u|xnbU{m33jl#Y z6c!W~0I3GE})6_3c$EJyI}cFNl8iZsXL+_P<$oafW3FORjwJ43e&kUA?2t%aF%fA61$of}>;JGL@57e;!fl1C`U>KkVY^|R=d+r?M zf7Xq<2O7c7l%|-s=1ppurnZU-zZBbcdMq6E=0jAw)!e)KEWUToUbLeYO*{LtE$?3U zDEiD{CFK&8Khy!a#))X|#wC4ioby1fR#zk-JXPak&0c2)_1ER^iK<#MC}-Mwh@6DM zKrp6%?AU1>9i>%u;hcEc>XvQLK>BKdK)G{xRRxb|p)a9XJ;uGY>2+p#Lk&+PW{{=K{lPq%;MMeJomzUxMLsA)em zd-Ww5^*uaaQjgKCrO+Q~D5azbNzM9h<6AZ;iJY&m;A&`DFm4$-BiuQs0iYSG*JI!};sMJ)$sJQ2iNe>50++7K4|gqJYmcBPzE zB`@5Z20tdVjlaFswH>khn#p6(*RNiQ-a$M>s#4~hu}VXiB>(GuV0OfBzLagvjQ0!G zrp%8wBFI-p_gyU~sRf*?M}fMmh1jsP1T#4Im{7KFT2vrk`MjD44@`9^*IH~cFspLWX>;MdJRjrt{zgz_q9ERzm&MV$#L%|ebY-rr@AO34 zwEX5x+)bo*bK)PDHQnVzIvuicmh5^TAt6nkDNs?rt>~>ndlBi6xQPz!(@6@(i0nqW z<*Mf)Ya{i(?W*3Jd^_q^7qGe03r98_VCUeUsc>#7)`nko)n3I!2#j|aw;j7P=4HNQ z)5Yt?hnC)?-)Z~Ce(Y4$PjkT>%F)%4NM>RppQL9r&hXa!jXOvc5tC^Aan7idXG+c7 z9IgznO82j|Yj0cnhBUDyOiB4apzBKN8;;92_}WqPBW4X9!^n_hYb8Y485M%iJ8HbS z$~KXEB`xX744upFg{a$Ai{UCmKNs1i9=p;Rh9i!-fg|Yn;sTPNG2S)0PB~@QuT^jS zDYTc1zg0?Sm~GFjTW46VrLsA=>Gt?awY#s=i}J`i+gZ%DQS(PCwVUn%FCWb91M`!1 zqPtf+3HC7#wMC9Og^27q%A0{Y@K1cfVqYLUfvqDy*!`QK&AnZN_fr=QW4I?X&qvKh zMKA1b`C!s`Y}4}})3OsKnV-wm5h_1S(=9D3C4MKyl@Rc9h%X^3E@f=f(&aB1o+@Pd zWcw`?m}cb0NACknU6ut}wNr(lrCe&9Yp-4U^6q>YraB9_etY*J(?JaEu0UEJh2j z#vebCMC^`t@2PEaTQQA`s=!am2OtI{+^mNgVFNf9+t3%tNz1og z>W@0CO5-Z6oQg{!wz8k2f{}gKR8>LR?fUWeRwA!)R#>WkmKnvK&*`#6R_;Y8c@v4!kB~W5 z<%>v8`^V-wXE%N19~KUZPQOBaavijHHz=1bmPYSjm_XjdFPWRBAHLtK>xul4yw~Yh ze|+nV%vbbJk>kOPdMndOi@1=}cMSTf)^W+nXZ;!KLxgyqFix+q7&^uKtyQ&ewg?L4 zpY&5|1}UOtYSI`QD2G21lg9~fUp6e}1WuuSkgCu3fs)&5ck&am(Q0wk%_jOj2y7Qi zpua33314#j;oH7>W-LSHT)w~IUGXV-Oe@z~^w5WUd8&#f3VDU2N;gsr<~6Nmv}zXD zFa7+)5}3@fA-DVJdyxJ&cjtjmn?_jkiAW*qtVDT^YfrN2ncot_X8Wm#Q0BeNoLlo{ z7arEF$W<4onS_j3XI8d2nbAleo5Ncxq>Ml40C(RaMD0|B&cd8g9V>c{fyl|ullI>9 z-ktNYGuKA2>aO7(ZHZ0&9j#oMs25gZ7E2!KQS)C6Y(pBWC53UJ%RPn71JA=uBBj4| zV%QmM!=l?4w!{Kyv#{dWJi3@Nb}6L<*@YLM^mqCkiKD%yOZk!65gnGDni&v+l zcPiFYY9yB>S3NfdqJkS+*~QGGspZ+#;Ks7jvBl+@mVL4ScjZ}%np&hBcg~r|XCjvY z1v`mht*M}0W0r>1%&mGM@@5(S6cL%|_O|uACo&kqFxGtanRjYWG7H`@`O)>_n{7Ns zHqU~5LEOs3<({_M=+dJ4je8>;9!~fzW?qE0tKgk_I+rD6q}$om?c8r$E%kHw8@l@d z%G-ThW5iC(%OV!B(LEXK`=O9Nwe1z{%;l&5R4g{l{q1%czTM~7`eOTsm0PH)dnANy zp&6>GG)ecn32q+Qte0%u4Q`lqZ3o)Rai|Fcz8PD;YEATCC6hkcNElh(kul*_R*5Kh zgFoHN5HPQhvPuK*4NGW;Q?PprEH%H zWu2j&^J$0QKo;p6sMbbDbmuWUNcTimK^3am#z%QXau0wP(D)*2;JEjrQH}jb%$&(xs37 zc>I$xpE}@Iv zF-oZ>`+%6vaCvKH4^;!Nn^Me_Rd4j{$v3$d1kgXlYOe@_hh6+s%id@76mmylNBdu_ zi!?@M(kph)gtJje1~f{5mj^ns8 zg?GR1h7Ql_)L2*WCR}6s47^7O)A2E{i$+RTdKMJ2c(mkfUkr6D)VV@MR;#;gV^*s! 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"table (gko)"_pair_table.html, "tersoff (gkio)"_pair_tersoff.html, "tersoff/mod (gko)"_pair_tersoff_mod.html, +"tersoff/mod/c (o)"_pair_tersoff_mod.html, "tersoff/zbl (gko)"_pair_tersoff_zbl.html, "tip4p/cut (o)"_pair_coul.html, "tip4p/long (o)"_pair_coul.html, "tri/lj"_pair_tri_lj.html, -"vashishta (o)"_pair_vashishta.html, +"vashishta (ko)"_pair_vashishta.html, "vashishta/table (o)"_pair_vashishta.html, "yukawa (go)"_pair_yukawa.html, "yukawa/colloid (go)"_pair_yukawa_colloid.html, diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt index cad3c5e65e..9e8c2a3b46 100644 --- a/doc/src/compute_pressure.txt +++ b/doc/src/compute_pressure.txt @@ -37,20 +37,18 @@ The pressure is computed by the formula where N is the number of atoms in the system (see discussion of DOF below), Kb is the Boltzmann constant, T is the temperature, d is the -dimensionality of the system (2 or 3 for 2d/3d), V is the system -volume (or area in 2d). -The second term is the virial, -dU/dV, computed within LAMMPS for all -pairwise as well as 2-body, 3-body, 4-body, many-body, and -long-range interactions, where r_i and f_i are the position and -force vector of atom i, and the big black dot indicates dot product. -When periodic boundary conditions are used, the summation includes -contributions from periodic images of the atoms in the central box, -which involves computing partial forces on local and ghost atoms. -A detailed description of how partial forces for 2-body and manybody -potentials are computed is provided in "(Thompson)"_#Thompson. -"Fixes"_fix.html that impose constraints -(e.g. the "fix shake"_fix_shake.html command) also contribute to the -virial term. +dimensionality of the system (2 or 3 for 2d/3d), and V is the system +volume (or area in 2d). The second term is the virial, equal to +-dU/dV, computed for all pairwise as well as 2-body, 3-body, 4-body, +manybody, and long-range interactions, where r_i and f_i are the +position and force vector of atom i, and the black dot indicates a dot +product. When periodic boundary conditions are used, N' necessarily +includes periodic image (ghost) atoms outside the central box, and the +position and force vectors of ghost atoms are thus included in the +summation. When periodic boundary conditions are not used, N' = N = +the number of atoms in the system. "Fixes"_fix.html that impose +constraints (e.g. the "fix shake"_fix_shake.html command) also +contribute to the virial term. A symmetric pressure tensor, stored as a 6-element vector, is also calculated by this compute. The 6 components of the vector are @@ -70,8 +68,9 @@ compute temperature or ke and/or the virial. The {virial} keyword means include all terms except the kinetic energy {ke}. Details of how LAMMPS computes the virial efficiently for the entire -system, including the effects of periodic boundary conditions is -discussed in "(Thompson)"_#Thompson. +system, including for manybody potentials and accounting for the +effects of periodic boundary conditions are discussed in +"(Thompson)"_#Thompson. The temperature and kinetic energy tensor is not calculated by this compute, but rather by the temperature compute specified with the diff --git a/doc/src/pair_tersoff_mod.txt b/doc/src/pair_tersoff_mod.txt index f74f322b1e..5e1c4131df 100644 --- a/doc/src/pair_tersoff_mod.txt +++ b/doc/src/pair_tersoff_mod.txt @@ -45,7 +45,6 @@ formulation of the V_ij term, where it contains an additional c0 term. :c,image(Eqs/pair_tersoff_mod_c.jpg) - The modified cutoff function f_C proposed by "(Murty)"_#Murty and having a continuous second-order differential is employed. The angular-dependent term g(theta) was modified to increase the diff --git a/doc/src/pair_vashishta.txt b/doc/src/pair_vashishta.txt index 7bd5a06aa8..902e6012f8 100644 --- a/doc/src/pair_vashishta.txt +++ b/doc/src/pair_vashishta.txt @@ -8,6 +8,7 @@ pair_style vashishta command :h3 pair_style vashishta/omp command :h3 +pair_style vashishta/kk command :h3 pair_style vashishta/table command :h3 pair_style vashishta/table/omp command :h3 diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp index 888f73455a..57f0a9cd4c 100644 --- a/src/USER-MISC/pair_agni.cpp +++ b/src/USER-MISC/pair_agni.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing author: Axel Kohlmeyer (Temple U) + Contributing authors: Axel Kohlmeyer (Temple U), Venkatesh Botu ------------------------------------------------------------------------- */ #include