te')); return $arr; } /* 遍历用户所有主题 * @param $uid 用户ID * @param int $page 页数 * @param int $pagesize 每页记录条数 * @param bool $desc 排序方式 TRUE降序 FALSE升序 * @param string $key 返回的数组用那一列的值作为 key * @param array $col 查询哪些列 */ function thread_tid_find_by_uid($uid, $page = 1, $pagesize = 1000, $desc = TRUE, $key = 'tid', $col = array()) { if (empty($uid)) return array(); $orderby = TRUE == $desc ? -1 : 1; $arr = thread_tid__find($cond = array('uid' => $uid), array('tid' => $orderby), $page, $pagesize, $key, $col); return $arr; } // 遍历栏目下tid 支持数组 $fid = array(1,2,3) function thread_tid_find_by_fid($fid, $page = 1, $pagesize = 1000, $desc = TRUE) { if (empty($fid)) return array(); $orderby = TRUE == $desc ? -1 : 1; $arr = thread_tid__find($cond = array('fid' => $fid), array('tid' => $orderby), $page, $pagesize, 'tid', array('tid', 'verify_date')); return $arr; } function thread_tid_delete($tid) { if (empty($tid)) return FALSE; $r = thread_tid__delete(array('tid' => $tid)); return $r; } function thread_tid_count() { $n = thread_tid__count(); return $n; } // 统计用户主题数 大数量下严谨使用非主键统计 function thread_uid_count($uid) { $n = thread_tid__count(array('uid' => $uid)); return $n; } // 统计栏目主题数 大数量下严谨使用非主键统计 function thread_fid_count($fid) { $n = thread_tid__count(array('fid' => $fid)); return $n; } ?>python - Is it possible to write off diagonal pressure tensor or viscosity in Amber? - Stack Overflow

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    python - Is it possible to write off diagonal pressure tensor or viscosity in Amber? - Stack Overflow

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    I have been trying to calculate the pressure tensor using AMBER simulation data. I have stored the force, velocity, and trajectory for each snapshot and attempted to compute the pressure tensor manually in Python using the Green-Kubo equation. As far as I understand, the mden file stores the diagonal components of the pressure tensor as Pres_x, Pres_y, and Pres_z in line number 3. However, when I compared my results with the values from the mden file (plotting Nsteps vs. Pres_X), there was no correlation.

    To ensure proper boundary conditions, I translated the trajectory within the simulation box before calculating the pressure tensor. My ultimate goal is to compute the viscosity, and I am simulating an ionic liquid system with 25,000 atoms under periodic boundary conditions (PBC) in a 90×90×90 ų simulation box.

    I am looking for guidance on the following:

    1. Is it possible to directly output the full (both diagonal and off-diagonal) pressure tensor or viscosity from an AMBER molecular dynamics simulation? If modifications to the source code are required, how should I proceed?
    2. Are there any detailed resources or documentation explaining how to compute the pressure tensor or viscosity from AMBER simulation data using post-processing methods based on velocity, force, and trajectory information? If anyone has experience with this, I would appreciate insights on how you approached it.

    Any hints, suggestions, or relevant references would be greatly appreciated. Thank you!

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