From 80c9e695a5149548438c865308657a5ef6608e80 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Mon, 11 Jul 2016 11:58:32 +0200
Subject: [PATCH] Removed IMD module
This module was not actually maintained.
In case someone is interested in restoring it, contact the developers
---
src/imd/.gitignore | 5 -
src/imd/ActionIMD.cpp | 286 ------------------------------------------
src/imd/Makefile | 28 -----
src/imd/module.type | 1 -
4 files changed, 320 deletions(-)
delete mode 100644 src/imd/.gitignore
delete mode 100644 src/imd/ActionIMD.cpp
delete mode 100644 src/imd/Makefile
delete mode 100644 src/imd/module.type
diff --git a/src/imd/.gitignore b/src/imd/.gitignore
deleted file mode 100644
index b6c9587b8..000000000
--- a/src/imd/.gitignore
+++ /dev/null
@@ -1,5 +0,0 @@
-/*.c
-/*.h
-/Makefile.conf
-/imdapi*
-!/module.type
diff --git a/src/imd/ActionIMD.cpp b/src/imd/ActionIMD.cpp
deleted file mode 100644
index 74c975d76..000000000
--- a/src/imd/ActionIMD.cpp
+++ /dev/null
@@ -1,286 +0,0 @@
-/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2016 The plumed team
- (see the PEOPLE file at the root of the distribution for a list of names)
-
- See http://www.plumed.org for more information.
-
- This file is part of plumed, version 2.
-
- plumed is free software: you can redistribute it and/or modify
- it under the terms of the GNU Lesser General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- plumed is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with plumed. If not, see <http://www.gnu.org/licenses/>.
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#include "../core/ActionRegister.h"
-#include "../core/ActionAtomistic.h"
-#include "../core/ActionPilot.h"
-#include "../core/PlumedMain.h"
-#include "../core/Atoms.h"
-#include "../tools/Exception.h"
-#include <unistd.h>
-
-extern "C" {
-#include "vmdsock.h"
-#include "imd.h"
-}
-
-
-namespace PLMD {
-
-//+PLUMEDOC GENERIC IMD
-/*
-Use interactive molecular dynamics with VMD
-
-\par Examples
-
-\verbatim
-# listen to port 1112 of localhost
-IMD PORT=1112
-\endverbatim
-\verbatim
-# listen to port 1112 of pippo
-IMD HOST=pippo PORT=1112
-\endverbatim
-\verbatim
-# listen to port 1112 of localhost and run only when connected
-IMD PORT=1112 WAIT
-\endverbatim
-
-\attention
-The IMB object only works if the IMD routines have been downloaded
-and properly linked with PLUMED
-
-*/
-//+ENDPLUMEDOC
-
-class IMD :
- public ActionAtomistic,
- public ActionPilot
- {
- std::string host;
- int port;
- bool wait;
- bool wrap;
- void* sock;
- void* clientsock;
- bool connected;
- std::vector<float> coord;
- std::vector<double> forces;
- int natoms;
- int transferRate;
- double fscale;
- void connect();
- void receive();
- void sendCoordinates();
-public:
- static void registerKeywords( Keywords& keys );
- void calculate();
- void apply();
- explicit IMD(const ActionOptions&);
- ~IMD(){};
-};
-
-PLUMED_REGISTER_ACTION(IMD,"IMD")
-
-void IMD::registerKeywords( Keywords& keys ){
- keys.addFlag("WAIT",false,"");
- keys.addFlag("NOWAIT",true,"");
- keys.addFlag("WRAP",false,"");
- keys.add("compulsory","HOST","");
- keys.add("compulsory","PORT","");
- keys.add("compulsory","FSCALE","1.0","");
-}
-
-IMD::IMD(const ActionOptions& ao):
- Action(ao),
- ActionAtomistic(ao),
- ActionPilot(ao),
- host("localhost"),
- port(0),
- wait(false),
- wrap(false),
- sock(NULL),
- clientsock(NULL),
- connected(false),
- transferRate(100),
- fscale(1.0)
-{
- natoms=plumed.getAtoms().getNatoms();
-
- std::vector<AtomNumber> index(natoms);
- for(int i=0;i<natoms;i++) index[i].setIndex(i);
- requestAtoms(index);
- coord.resize(natoms*3,float(0.0));
- forces.resize(natoms*3,0.0);
-
- parseFlag("WAIT",wait);
- bool nowait=false;
- parseFlag("NOWAIT",nowait);
- if(nowait)wait=false;
- parseFlag("WRAP",wrap);
- parse("PORT",port);
- parse("HOST",host);
- parse("FSCALE",fscale);
-
- checkRead();
-
- log.printf(" with host %s\n",host.c_str());
- log.printf(" with port %d\n",port);
- if(wait) log.printf(" waiting for a connection\n");
- else log.printf(" not waiting for a connection\n");
- if(wrap) log.printf(" wrapping atoms\n");
- else log.printf(" not wrapping atoms\n");
- log.printf(" WMD forces will be scaled by %f\n",fscale);
-
- if(comm.Get_rank()==0){
- vmdsock_init();
- sock = vmdsock_create();
- vmdsock_bind(sock, port);
- vmdsock_listen(sock);
- }
-
- connect();
-}
-
-void IMD::connect(){
- if(comm.Get_rank()==0) {
- if(wait && clientsock==NULL)
- fprintf(stderr,"Waiting for IMD connection on %s:%d...\n", host.c_str(), port);
- do{
- if (vmdsock_selread(sock,00) > 0) {
- clientsock = vmdsock_accept(sock);
- if (imd_handshake(clientsock)) {
- clientsock = NULL;
- };
- sleep(1);
- int length;
- if(clientsock){
- if (vmdsock_selread(clientsock, 0) != 1 ||
- imd_recv_header(clientsock, &length) != IMD_GO) {
- clientsock = NULL;
- }
- }
- }
- } while(wait && clientsock==NULL);
- connected=(clientsock!=NULL);
- int c=connected;
- comm.Bcast(&c,1,0);
- } else {
- int c;
- comm.Bcast(&c,1,0);
- connected=c;
- }
-}
-
-void IMD::receive(){
-
- if(!connected) return;
-
- if(clientsock){
- IMDType type;
- int length;
- int itype;
- while (vmdsock_selread(clientsock,0) > 0) {
- type = imd_recv_header(clientsock, &length);
- if(type==IMD_MDCOMM){
- int32* vmd_atoms = new int32[length];
- float* vmd_forces = new float[3*length];
- imd_recv_mdcomm(clientsock, length, vmd_atoms, vmd_forces);
- for(int i=0;i<length;i++){
- forces[3*vmd_atoms[i]+0]=vmd_forces[3*i+0];
- forces[3*vmd_atoms[i]+1]=vmd_forces[3*i+1];
- forces[3*vmd_atoms[i]+2]=vmd_forces[3*i+2];
- }
- delete [] vmd_atoms;
- delete [] vmd_forces;
- itype=0;
- comm.Bcast(&itype,1,0);
- comm.Bcast(&forces[0],forces.size(),0);
- }else if(type==IMD_DISCONNECT){
- vmdsock_destroy(clientsock);
- clientsock=NULL;
- for(unsigned i=0;i<forces.size();i++) forces[i]=0.0;
- connected=false;
- itype=1;
- comm.Bcast(&itype,1,0);
- break;
- }else if(type==IMD_TRATE){
- if(length<1) length=1;
- itype=2;
- log.printf("IMD: setting transfer rate to %d\n",length);
- transferRate=length;
- comm.Bcast(&itype,1,0);
- comm.Bcast(&transferRate,1,0);
- }else if(type==IMD_KILL){
- log.printf("IMD: killing simulation\n");
- itype=3;
- comm.Bcast(&itype,1,0);
- plumed.exit();
- }
- }
- itype=-1;
- comm.Bcast(&itype,1,0);
- }
-
- if(comm.Get_rank()!=0){
- int itype;
- while(true){
- comm.Bcast(&itype,1,0);
- if(itype==-1)break;
- else if(itype==0) comm.Bcast(&forces[0],forces.size(),0);
- else if(itype==1) {
- for(unsigned i=0;i<forces.size();i++) forces[i]=0.0;
- connected=false;
- }
- else if(itype==2) comm.Bcast(&transferRate,1,0);
- else if(itype==3) plumed.exit();
- else plumed_error();
- }
- }
-
-}
-
-void IMD::calculate(){
- if(comm.Get_rank()==0 && connected && plumed.getStep()%transferRate==0 && vmdsock_selwrite(clientsock,0)) {
- double scale=10.0*plumed.getAtoms().getUnits().getLength();
- Vector ref;
- for(int i=0;i<natoms;i++){
- Vector pos=getPosition(i);
- if(wrap) pos=pbcDistance(ref,pos);
- coord[3*i+0]=static_cast<float>((pos[0]*scale));
- coord[3*i+1]=static_cast<float>((pos[1]*scale));
- coord[3*i+2]=static_cast<float>((pos[2]*scale));
- }
- imd_send_fcoords(clientsock,natoms,&coord[0]);
- }
-}
-
-void IMD::apply(){
-
- std::vector<Vector> & f(modifyForces());
-
- const double scale=4.184/plumed.getAtoms().getUnits().getEnergy()
- /(0.1/plumed.getAtoms().getUnits().getLength())*fscale;
-
- for(unsigned i=0;i<f.size();i++){
- f[i][0]=forces[3*i+0]*getStride()*scale;
- f[i][1]=forces[3*i+1]*getStride()*scale;
- f[i][2]=forces[3*i+2]*getStride()*scale;
- }
-
- connect();
- receive();
-
-}
-
-
-}
-
diff --git a/src/imd/Makefile b/src/imd/Makefile
deleted file mode 100644
index 08656a8db..000000000
--- a/src/imd/Makefile
+++ /dev/null
@@ -1,28 +0,0 @@
-# include the machine dependent configuration
-ifneq ($(MAKECMDGOALS),clean)
- -include ../../Makefile.conf
-endif
-
-all: libimd.$(SOEXT)
-
-libimd.$(SOEXT): imd.o vmdsock.o ActionIMD.o
- $(LDSO) -o $@ $^ # -lnsl
-
-vmdsock.c imd.c vmdsock.h imd.h: imdapi.tar.gz
- tar xzOf imdapi.tar.gz imdapi/$@ > $@
-
-vmdsock.o imd.o: vmdsock.h imd.h
-
-imdapi.tar.gz:
- wget http://www.ks.uiuc.edu/Research/vmd/imd/code/imdapi.tar.gz
-
-
-clean:
- rm -fr imdapi.tar.gz *.c *.h *.$(SOEXT) *.o
-
-obj: all
-
-links:
- # do nothing
-
-
diff --git a/src/imd/module.type b/src/imd/module.type
deleted file mode 100644
index de8327303..000000000
--- a/src/imd/module.type
+++ /dev/null
@@ -1 +0,0 @@
-default-off
--
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